10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C.  20549

FORM 10-Q

x Quarterly report pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 for the quarterly period ended April 8, 2012; or

o Transition report pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 for the transition period from __________ to __________.

Commission File Number:  0-19797

WHOLE FOODS MARKET, INC.

(Exact name of registrant as specified in its charter)

Texas	74-1989366
(State of	(IRS employer
incorporation)	identification no.)

550 Bowie Street

Austin, Texas 78703

(Address of principal executive offices)

512-477-4455

(Registrant’s telephone number, including area code)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.  Yes x  No o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).  Yes x  No o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company (as defined in Rule 12b-2 of the Exchange Act).

Large accelerated filer x	Accelerated filer o
Non-accelerated filer o	Smaller reporting company o
(Do not check if a smaller reporting company)

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).  Yes o  No x

The number of shares of the registrant’s common stock, no par value, outstanding as of May 11, 2012 was 183,563,879 shares.

Whole Foods Market, Inc.

Form 10-Q

Table of Contents

	Page Number
Part I. Financial Information
Item 1. Financial Statements
Consolidated Balance Sheets (unaudited), April 8, 2012 and September 25, 2011	3
Consolidated Statements of Operations (unaudited), for the twelve and twenty-eight weeks ended April 8, 2012 and April 10, 2011	4
Consolidated Statements of Shareholders’ Equity and Comprehensive Income (unaudited), for the twenty-eight weeks ended April 8, 2012 and fiscal year ended September 25, 2011	5
Consolidated Statements of Cash Flows (unaudited), for the twenty-eight weeks ended April 8, 2012 and April 10, 2011	6
Notes to Consolidated Financial Statements (unaudited)	7
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations	14
Item 4. Controls and Procedures	20
Part II. Other Information
Item 1. Legal Proceedings	21
Item 5. Other Information	21
Item 6. Exhibits	22
Signature	23

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Part I. Financial Information

Item 1. Financial Statements

Whole Foods Market, Inc.

Consolidated Balance Sheets (unaudited)

April 8, 2012 and September 25, 2011

(In thousands)

Assets	2012			2011
Current assets:
Cash and cash equivalents	$	175,375		$	212,004
Short-term investments - available-for-sale securities	881,945			442,320
Restricted cash	104,942			91,956
Accounts receivable	189,717			175,310
Merchandise inventories	365,619			336,799
Prepaid expenses and other current assets	59,813			73,579
Deferred income taxes	122,766			121,176
Total current assets	1,900,177			1,453,144
Property and equipment, net of accumulated depreciation and amortization	2,053,507			1,997,212
Long-term investments - available-for-sale securities	139,956			52,815
Goodwill	662,938			662,938
Intangible assets, net of accumulated amortization	66,047			67,234
Deferred income taxes	43,047			50,148
Other assets	8,447			8,584
Total assets	$	4,874,119		$	4,292,075
Liabilities and Shareholders’ Equity
Current liabilities:
Current installments of capital lease obligations	$	346		$	466
Accounts payable	243,627			236,913
Accrued payroll, bonus and other benefits due team members	300,501			281,587
Dividends payable	25,610			17,827
Other current liabilities	382,139			342,568
Total current liabilities	952,223			879,361
Long-term capital lease obligations, less current installments	18,882			17,439
Deferred lease liabilities	395,881			353,776
Other long-term liabilities	52,175			50,194
Total liabilities	1,419,161			1,300,770
Shareholders’ equity:
Common stock, no par value, 600,000 and 300,000 shares authorized; 182,980 and 178,886 shares issued; 182,923 and 178,886 shares outstanding at 2012 and 2011, respectively	2,399,979			2,120,972
Common stock in treasury, at cost	(3,599		)	—
Accumulated other comprehensive income (loss)	2,932			(164		)
Retained earnings	1,055,646			870,497
Total shareholders’ equity	3,454,958			2,991,305
Commitments and contingencies
Total liabilities and shareholders’ equity	$	4,874,119		$	4,292,075

The accompanying notes are an integral part of these consolidated financial statements.

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Whole Foods Market, Inc.

Consolidated Statements of Operations (unaudited)

(In thousands, except per share amounts)

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Sales	$	2,670,282	$	2,350,518	$	6,061,222	$	5,354,173
Cost of goods sold and occupancy costs	1,700,574		1,513,446		3,913,397		3,478,616
Gross profit	969,708		837,072		2,147,825		1,875,557
Direct store expenses	681,771		608,737		1,552,696		1,399,366
General and administrative expenses	86,760		75,661		190,276		164,172
Pre-opening expenses	10,496		9,543		20,901		18,183
Relocation, store closure and lease termination costs	1,298		1,003		4,231		4,149
Operating income	189,383		142,128		379,721		289,687
Investment and other income, net of interest	2,254		658		4,633		977
Income before income taxes	191,637		142,786		384,354		290,664
Provision for income taxes	73,972		52,851		148,362		111,999
Net income	$	117,665	$	89,935	$	235,992	$	178,665
Basic earnings per share	$	0.65	$	0.51	$	1.31	$	1.03
Weighted average shares outstanding	182,161		174,686		180,649		173,606
Diluted earnings per share	$	0.64	$	0.51	$	1.29	$	1.02
Weighted average shares outstanding, diluted basis	184,603		177,124		182,841		175,614
Dividends declared per common share	$	0.14	$	0.10	$	0.28	$	0.20

The accompanying notes are an integral part of these consolidated financial statements.

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Whole Foods Market, Inc.

Consolidated Statementsof Shareholders’ Equityand Comprehensive Income (unaudited)

Twenty-eight weeks endedApril 8, 2012 and fiscal year ended September 25, 2011

(In thousands)

	Shares outstanding		Common stock		Common stock in treasury			Accumulated other comprehensive income (loss)			Retained earnings			Total shareholders’ equity
Balances at September 26, 2010	172,033		$	1,773,897	$	—		$	791		$	598,570		$	2,373,258
Net income	—		—		—			—			342,612			342,612
Foreign currency translation adjustments	—		—		—			(1,209		)	—			(1,209		)
Reclassification adjustments for amounts included in net income	—		—		—			245			—			245
Change in unrealized gains and losses, net of income taxes	—		—		—			9			—			9
Comprehensive income														341,657
Dividends ($0.40 per common share)	—		—		—			—			(70,447		)	(70,447		)
Issuance of common stock pursuant to team member stock plans	6,857		301,591		—			—			—			301,591
Excess tax benefit related to exercise of team member stock options	—		18,225		—			—			—			18,225
Share-based payment expense	—		27,259		—			—			—			27,259
Other	(4	)	—		—			—			(238		)	(238		)
Balances at September 25, 2011	178,886		2,120,972		—			(164		)	870,497			2,991,305
Net income	—		—		—			—			235,992			235,992
Foreign currency translation adjustments	—		—		—			3,111			—			3,111
Change in unrealized gains and losses, net of income taxes	—		—		—			(15		)	—			(15		)
Comprehensive income														239,088
Dividends ($0.28 per common share)	—		—		—			—			(50,843		)	(50,843		)
Issuance of common stock pursuant to team member stock plans	4,094		232,860		—			—			—			232,860
Purchase of treasury stock	(57	)	—		(3,599		)	—			—			(3,599		)
Excess tax benefit related to exercise of team member stock options	—		26,388		—			—			—			26,388
Share-based payment expense	—		19,759		—			—			—			19,759
Balances at April 08, 2012	182,923		$	2,399,979	$	(3,599	)	$	2,932		$	1,055,646		$	3,454,958

The accompanying notes are an integral part of these consolidated financial statements.

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Whole Foods Market, Inc.

Consolidated Statementsof Cash Flows (unaudited)

(In thousands)

	Twenty-eight weeks ended
	April 8, 2012			April 10, 2011
Cash flows from operating activities
Net income	$	235,992		$	178,665
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization	162,509			152,903
Loss on disposition of fixed assets	1,103			914
Share-based payment expense	19,759			12,848
LIFO expense	1,000			3,000
Deferred income tax expense	5,624			15,747
Excess tax benefit related to exercise of team member stock options	(15,481		)	(9,251		)
Deferred lease liabilities	37,429			24,110
Other	4,780			202
Net change in current assets and liabilities:
Accounts receivable	(18,816		)	(24,991		)
Merchandise inventories	(29,489		)	(20,474		)
Prepaid expenses and other current assets	14,278			(7,310		)
Accounts payable	6,334			20,176
Accrued payroll, bonus and other benefits due team members	18,718			9,580
Other current liabilities	71,101			46,457
Net change in other long-term liabilities	1,840			241
Net cash provided by operating activities	516,681			402,817
Cash flows from investing activities
Development costs of new locations	(114,549		)	(89,451		)
Other property and equipment expenditures	(98,729		)	(80,130		)
Purchase of available-for-sale securities	(1,321,589		)	(780,154		)
Sale of available-for-sale securities	789,432			731,306
Decrease (increase) in restricted cash	(12,986		)	17
Other investing activities	(1,614		)	(1,576		)
Net cash used in investing activities	(760,035		)	(219,988		)
Cash flows from financing activities
Common stock dividends paid	(43,057		)	(17,348		)
Issuance of common stock	237,004			153,067
Purchase of treasury stock	(3,599		)	—
Excess tax benefit related to exercise of team member stock options	15,481			9,251
Payments on long-term debt and capital lease obligations	(113		)	(300,123		)
Net cash provided by (used in) financing activities	205,716			(155,153		)
Effect of exchange rate changes on cash and cash equivalents	1,009			2,431
Net change in cash and cash equivalents	(36,629		)	30,107
Cash and cash equivalents at beginning of period	212,004			131,996
Cash and cash equivalents at end of period	$	175,375		$	162,103
Supplemental disclosures of cash flow information:
Interest paid	$	1,616		$	14,002
Federal and state income taxes paid	$	91,172		$	109,611

The accompanying notes are an integral part of these consolidated financial statements.

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Whole Foods Market, Inc.

Notes to Consolidated Financial Statements (unaudited)

April 8, 2012

(1) Basis of Presentation

The accompanying unaudited consolidated financial statements of Whole Foods Market, Inc. and its consolidated subsidiaries (collectively “Whole Foods Market,” “Company,” or “We”) have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”) for interim financial statements and with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. The information included in this Form 10-Q should be read in conjunction with Management’s Discussion and Analysis, the consolidated financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 25, 2011. In the opinion of management, the accompanying consolidated financial statements reflect all adjustments, consisting of normal recurring accruals, considered necessary for a fair presentation. Where appropriate, we have reclassified prior years’ financial statements to conform to current year presentation. Interim results are not necessarily indicative of results for any other interim period or for a full fiscal year. The Company reports its results of operations on a 52- or 53-week fiscal year ending on the last Sunday in September. The first fiscal quarter is 16 weeks, the second and third quarters each are 12 weeks, and the fourth quarter is 12 or 13 weeks. Fiscal year 2012 is a 53-week year and fiscal year 2011 was a 52-week year. The Company has one operating segment and a single reportable segment, natural and organic foods supermarkets. The following is a summary of percentage sales by geographic area for the twelve and twenty-eight weeks ended:

	April 8, 2012		April 10, 2011
Sales:
United States	96.8	%	96.9	%
Canada and United Kingdom	3.2		3.1
Total sales	100.0	%	100.0	%

The following is a summary of the percentage of net long-lived assets by geographic area as of the dates indicated:

	April 8, 2012		September 25, 2011
Long-lived assets, net:
United States	95.7	%	95.9	%
Canada and United Kingdom	4.3		4.1
Total long-lived assets, net	100.0	%	100.0	%

(2) Recent Accounting Pronouncements

In December 2010, the Financial Accounting Standards Board (“FASB”) issued amended guidance within Accounting Standards Codification (“ASC”) 805, “Business Combinations,” which updates previous guidance on this topic and applies to all material transactions. The amendments specify that if a public entity presents comparative financial statements, the entity should disclose revenue and earnings of the combined entity as though the business combination(s) had occurred as of the beginning of the comparable prior annual reporting period only. Additional amendments expand supplemental pro forma disclosures to include a description of the nature and amount of material, nonrecurring pro forma adjustments directly attributable to the business combination included in the reported pro forma revenue and earnings. The updated guidance is effective for fiscal years beginning after December 15, 2010 and is applied prospectively to business combinations completed on or after that date. The provisions are effective for the Company’s fiscal year ending September 30, 2012. We do not expect the adoption of these provisions to have a significant effect on our consolidated financial statements.

In June 2011, the FASB issued Accounting Standards Update (“ASU”) No. 2011-05, “Presentation of Comprehensive Income,” which amends ASC 220, “Comprehensive Income.” The amended guidance requires that all nonowner changes in stockholders’ equity be presented in either a single statement of comprehensive income or two separate but consecutive statements. The objective of these amendments is to improve the comparability, consistency, and transparency of financial reporting and to increase the prominence of items reported in other comprehensive income. In December 2011, the FASB issued ASU No. 2011-12, “Deferral of the Effective Date for Amendments to the Presentation of Reclassifications of Items Out of Accumulated Other Comprehensive Income in Accounting Standards Update No. 2011-05,” which defers the implementation requirement in ASU No. 2011-05 to present on the face of the financial statements the effects of reclassifications out of accumulated other comprehensive income on the components of net income and other comprehensive income. The amended guidance specifies that entities should continue to report reclassifications out of accumulated other comprehensive income consistent with

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presentation requirements in effect before ASU No. 2011-05. The guidance provided in ASU No. 2011-05 and ASU No. 2011-12 is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. The provisions are effective for the Company’s first quarter of the fiscal year ending September 29, 2013.

(3) Fair Value Measurements

Effective January 16, 2012, the Company adopted ASU No. 2011-04, “Amendments to Achieve Common Fair Value Measurement and Disclosure Requirements in U.S. GAAP and IFRSs,” which amends ASC 820, “Fair Value Measurement.” The adoption of ASU No. 2011-04, which primarily consists of clarification and wording changes to existing fair value measurement and disclosure requirements, did not have an impact on the Company’s consolidated financial statements.

Assets and Liabilities Measured at Fair Value on a Recurring Basis

The Company holds money market fund investments that are classified as cash equivalents or restricted cash that are measured at fair value on a recurring basis based on quoted prices in active markets for identical assets. The Company also holds available-for-sale securities generally consisting of state and local municipal obligations and variable rate demand notes which hold high credit ratings. These instruments are valued using a series of multi-dimensional relational models and series of matrices with standard inputs obtained from readily available pricing sources and other observable market data, such as benchmark yields and base spread. Investments are stated at fair value with unrealized gains and losses, net of related tax effect, included as a component of shareholders’ equity until realized. Declines in fair value below the Company’s carrying value deemed to be other-than-temporary are charged against net earnings.

The carrying amounts of trade and other accounts receivable, trade accounts payable, accrued payroll, bonuses and team member benefits, and other accrued expenses approximate fair value because of the short maturity of those instruments. Store closure reserves and estimated workers’ compensation claims are recorded at net present value to approximate fair value.

The Company held the following financial assets at fair value, based on the hierarchy input levels indicated, on a recurring basis (in thousands):

April 8, 2012	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Cash equivalents:
Money market fund	$	20,078	$	—	$	—	$	20,078
Municipal bonds	—		8,411		—		8,411
Restricted cash:
Money market fund	104,942		—		—		104,942
Marketable securities - available-for-sale:
Municipal bonds	—		458,317		—		458,317
Corporate bonds	—		5,309		—		5,309
Commercial paper	—		22,985		—		22,985
Variable rate demand notes	—		535,290		—		535,290
Total	$	125,020	$	1,030,312	$	—	$	1,155,332

September 25, 2011	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Cash equivalents:
Money market fund	$	59,157	$	—	$	—	$	59,157
Municipal bonds	—		3,791		—		3,791
Commercial paper	—		12,998		—		12,998
Restricted cash:
Money market fund	91,956		—		—		91,956
Marketable securities - available-for-sale:
Municipal bonds	—		316,662		—		316,662
Corporate bonds	—		5,361		—		5,361
Commercial paper	—		67,964		—		67,964
Variable rate demand notes	—		105,148		—		105,148
Total	$	151,113	$	511,924	$	—	$	663,037

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Assets Measured at Fair Value on a Nonrecurring Basis

The Company evaluates long-lived assets for impairment whenever events or changes in circumstances, such as unplanned negative cash flow or short lease life, indicate that the carrying amount of an asset may not be recoverable. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset to fair value. The fair value is determined using management’s best estimate based on a discounted cash flow model based on future store operating results using internal projections. Fair value adjustments, based on hierarchy input Level 3, reduced the carrying value of related property and equipment to zero and were included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Direct store expenses	$	1	$	9	$	20	$	501
General and administrative expenses	1,178		—		1,178		—
Relocation, store closure and lease term costs	—		13		—		80
Total impairment of long-lived assets	$	1,179	$	22	$	1,198	$	581

(4) Investments

The Company holds investments in marketable securities, generally municipal bonds, corporate bonds, commercial paper and variable rate demand notes, that are classified as either short- or long-term available-for-sale securities. The Company held the following investments as of the dates indicated (in thousands):

April 8, 2012	Adjusted cost		Unrealized gains		Unrealized losses			Fair value
Short-term marketable securities - available-for-sale:
Municipal bonds	$	323,559	$	165	$	(54	)	$	323,670
Commercial paper	22,975		10		—			22,985
Variable rate demand notes	535,290		—		—			535,290
Total short-term marketable securities	$	881,824	$	175	$	(54	)	$	881,945
Long-term marketable securities - available-for-sale:
Municipal bonds	$	134,506	$	167	$	(26	)	$	134,647
Corporate bonds	5,270		39		—			5,309
Total long-term marketable securities	$	139,776	$	206	$	(26	)	$	139,956

September 25, 2011	Adjusted cost		Unrealized gains		Unrealized losses			Fair value
Short-term marketable securities - available-for-sale:
Municipal bonds	$	268,945	$	279	$	(16	)	$	269,208
Commercial paper	67,950		14		—			67,964
Variable rate demand notes	105,148		—		—			105,148
Total short-term marketable securities	$	442,043	$	293	$	(16	)	$	442,320
Long-term marketable securities - available-for-sale:
Municipal bonds	$	47,387	$	77	$	(10	)	$	47,454
Corporate bonds	5,345		16		—			5,361
Total long-term marketable securities	$	52,732	$	93	$	(10	)	$	52,815

At April 8, 2012 and September 25, 2011 available-for-sale securities totaling approximately $163.7 million and $74.5 million, respectively, were in unrealized loss positions.

At April 8, 2012, the average effective maturity of the Company’s short- and long-term investments was approximately 2 months and 16 months, respectively, compared to approximately 4 months and 15 months, respectively at September 25, 2011.

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(5) Intangible Assets

The components of intangible assets were as follows (in thousands):

	April 8, 2012					September 25, 2011
	Gross carrying amount		Accumulated amortization			Gross carrying amount		Accumulated amortization
Definite-lived contract-based	$	96,758	$	(33,290	)	$	96,019	$	(31,660	)
Definite-lived marketing-related and other	1,547		(1,019		)	1,547		(420		)
Indefinite-lived contract-based	2,051					1,748
	$	100,356	$	(34,309	)	$	99,314	$	(32,080	)

Amortization associated with intangible assets totaled approximately $1.3 million and $3.1 million for the twelve and twenty-eight weeks ended April 8, 2012, respectively, and approximately $2.0 million and $3.8 million, respectively, for the same periods of the prior fiscal year. Future amortization associated with the net carrying amount of intangible assets is estimated to be approximately as follows (in thousands):

Remainder of fiscal year 2012	$	2,601
Fiscal year 2013	4,578
Fiscal year 2014	4,529
Fiscal year 2015	4,405
Fiscal year 2016	4,280
Future fiscal years	43,603
	$	63,996

(6) Reserves for Closed Properties

Following is a summary of store closure reserve activity during the twenty-eight weeks ended April 8, 2012 and fiscal year ended September 25, 2011 (in thousands):

	April 8, 2012			September 25, 2011
Beginning balance	$	44,702		$	59,298
Additions	1,964			4,706
Usage	(5,154		)	(17,805		)
Adjustments	1,203			(1,497		)
Ending balance	$	42,715		$	44,702

Additions to store closure reserves relate to the accretion of interest on existing reserves and new closures. Usage included approximately $5.2 million in ongoing cash rental payments during the twenty-eight weeks ended April 8, 2012. During the fiscal year ended September 25, 2011, usage included approximately $10.1 million in ongoing cash rental payments and approximately $7.7 million in termination fees related to certain idle properties. Additionally, the Company recorded reserve adjustments of approximately $3.7 million during the fiscal year ended September 25, 2011, offset to goodwill.

(7) Long-Term Debt

The Company has a $350 million revolving line of credit that extends to August 28, 2012. The Company’s obligations under the facility are secured by liens on certain of the Company’s assets, including stock of its subsidiaries. The credit agreement contains certain affirmative covenants including maintenance of certain financial ratios and certain negative covenants including limitations on additional indebtedness and payments as defined by the agreement. At April 8, 2012 the Company was in compliance with all applicable debt covenants. At April 8, 2012 and September 25, 2011 the Company had no amounts drawn under this agreement. The amount available to the Company under the agreement was $350 million at April 8, 2012. The amount available to the Company at September 25, 2011 was effectively reduced to approximately $348.6 million by outstanding letters of credit totaling approximately $1.4 million. The Company had outstanding a $700 million, five-year term loan agreement due in 2012, with an outstanding balance of $490 million at September 26, 2010. During the twenty-eight weeks ended April 10, 2011, the Company repaid $300 million on the term loan and repaid the remainder throughout fiscal year 2011.

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(8) Income Taxes

Income taxes for both the twelve and twenty-eight weeks ended April 8, 2012 resulted in an effective tax rate of approximately 38.6%, compared to approximately 37.0% and 38.5%, respectively, for the same periods of the prior fiscal year. At April 8, 2012, income taxes payable totaled approximately $10.3 million compared to an income tax receivable of approximately $14.8 million at September 25, 2011.

(9) Shareholders’ Equity

Dividends per Common Share

During the twelve weeks ended April 8, 2012, the Company’s Board of Directors declared a cash dividend to shareholders of $0.14 per common share, payable on April 17, 2012 to shareholders of record on April 5, 2012. Approximately $25.6 million was included in the “Dividends payable” line item on the Consolidated Balance Sheets at April 8, 2012. During fiscal year 2011, the Company’s Board of Directors declared cash dividends to shareholders totaling $0.40 per common share resulting in dividend payments of approximately $70.4 million, of which approximately $17.8 million was included in the “Dividends payable” line item on the Consolidated Balance Sheets at September 25, 2011.

Common Stock

During the twelve weeks ended April 8, 2012, the Company approved an increase in the number of authorized shares of the Company’s common stock from 300 million to 600 million.

Treasury Stock

During the first quarter of fiscal year 2012, the Company’s Board of Directors authorized a $200 million stock repurchase program through November 1, 2013. The Company repurchased 56,500 shares of Company common stock on the open market during the first quarter of fiscal year 2012. The average price per share paid for shares held in treasury at April 8, 2012 was $63.70, for a total of approximately $3.6 million. The specific timing and repurchase of future amounts will vary based on market conditions, securities law limitations and other factors and will be made using the Company’s available resources. The repurchase program may be suspended or discontinued at any time at the Company’s discretion.

Comprehensive Income

The Company’s comprehensive income was comprised of: net income; unrealized gains and losses on investments; unrealized gains and losses on cash flow hedge instruments, including reclassification adjustments of unrealized losses to net income related to ongoing interest payments; and foreign currency translation adjustments, net of income taxes. Comprehensive income was as follows (in thousands):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012			April 10, 2011
Net income	$	117,665	$	89,935	$	235,992		$	178,665
Foreign currency translation adjustments	2,753		3,139		3,111			5,389
Reclassification adjustments for amounts included in net income	—		—		—			245
Change in unrealized gains and losses, net of income taxes	8		239		(15		)	(17		)
Comprehensive income	$	120,426	$	93,313	$	239,088		$	184,282

(10) Earnings per Share

The computation of basic earnings per share is based on the number of weighted average common shares outstanding during the period. The computation of diluted earnings per share includes the dilutive effect of common stock equivalents consisting of incremental common shares deemed outstanding from the assumed exercise of stock options.

11

A reconciliation of the numerators and denominators of the basic and diluted earnings per share calculations follows (in thousands, except per share amounts):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Net income (numerator for basic and diluted earnings per share)	$	117,665	$	89,935	$	235,992	$	178,665
Weighted average common shares outstanding (denominator for basic earnings per share)	182,161		174,686		180,649		173,606
Potential common shares outstanding:
Incremental shares from assumed exercise of stock options	2,442		2,438		2,192		2,008
Weighted average common shares outstanding and potential additional common shares outstanding (denominator for diluted earnings per share)	184,603		177,124		182,841		175,614
Basic earnings per share	$	0.65	$	0.51	$	1.31	$	1.03
Diluted earnings per share	$	0.64	$	0.51	$	1.29	$	1.02

For the twelve and twenty-eight weeks ended April 8, 2012 the number of stock options excluded from the computation of diluted earnings per share due to their antidilutive effect was not material. The computation of diluted earnings per share for the twelve and twenty-eight weeks ended April 10, 2011 does not include options to purchase approximately 4.9 million shares and 6.8 million shares of common stock due to their antidilutive effect.

(11) Share-Based Payments

Total share-based payment expense before income taxes recognized during the twelve and twenty-eight weeks ended April 8, 2012 was approximately $8.5 million and $19.8 million, respectively. Share-based payment expense before income taxes recognized during the twelve and twenty-eight weeks ended April 10, 2011 was approximately $5.5 million and $12.8 million, respectively. Share-based payment expense was included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended						Twenty-eight weeks ended
	April 8, 2012			April 10, 2011			April 8, 2012			April 10, 2011
Cost of goods sold and occupancy costs	$	372		$	288		$	945		$	658
Direct store expenses	4,473			2,894			10,363			6,619
General and administrative expenses	3,697			2,307			8,451			5,571
Share-based payment expense before income taxes	8,542			5,489			19,759			12,848
Income tax benefit	(3,236		)	(1,999		)	(7,454		)	(4,870		)
Net share-based payment expense	$	5,306		$	3,490		$	12,305		$	7,978

At April 8, 2012 and September 25, 2011, approximately 11.8 million shares and 11.7 million shares of the Company’s common stock, respectively, were available for future stock incentive grants. At April 8, 2012 and September 25, 2011, there was approximately $75.1 million and $97.4 million of unrecognized share-based payment expense, respectively, related to nonvested stock options, net of estimated forfeitures, related to approximately 6.4 million shares and 6.5 million shares, respectively. We anticipate this expense to be recognized over a weighted average period of approximately three years.

(12) Commitments and Contingencies

The Company is exposed to claims and litigation matters arising in the ordinary course of business and uses various methods to resolve these matters in a manner that we believe best serves the interests of our stakeholders. Our primary contingencies are associated with insurance and self-insurance obligations and litigation matters. Estimation of our insurance and self-insurance liabilities requires significant judgments, and actual claim settlements and associated expenses may differ from our current provisions for loss. We have exposures to loss contingencies arising from pending or threatened litigation for which assessing and estimating the outcomes of these matters involve substantial uncertainties.

12

On October 27, 2008, Whole Foods Market was served with the complaint in Kottaras v. Whole Foods Market, Inc., a putative class action filed in the United States District Court for the District of Columbia, seeking treble damages, equitable, injunctive, and declaratory relief and alleging that the acquisition and merger between Whole Foods Market and Wild Oats violates various provisions of the federal antitrust laws. During the first quarter of fiscal year 2012, the federal district judge denied the plaintiff’s motion for class certification. Currently that decision is being appealed. The Company has not accrued any loss related to the outcome of this case as of April 8, 2012.

The Company evaluates contingencies on an ongoing basis and has established loss provisions for matters in which losses are probable and the amount of loss can be reasonably estimated. Insurance and legal settlement liabilities are included in the “Other current liabilities” line item on the Consolidated Balance Sheets. We believe the recorded reserves in our consolidated financial statements are adequate in light of the probable and estimable liabilities.

(13) Related Party Transactions

The Company provides ongoing support to two independent non-profit organizations: Whole Planet Foundation and Whole Kids Foundation (the “Foundations”). Whole Planet Foundation’s mission is to empower the poor through microcredit, with a focus on developing-world communities that supply the Company’s stores with product. Whole Kids Foundation is a non-profit organization dedicated to improving children’s nutrition through partnerships with schools, educators, and other organizations. Members of the Company’s management comprise the Board of Directors of each of the Foundations. Additionally, the Company provides administrative support and covers all operating costs and the overhead budget of the Foundations.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

Forward-looking Statements

We wish to caution you that there are risks and uncertainties that could cause our actual results to be materially different from those indicated by forward-looking statements that we make from time to time in filings with the Securities and Exchange Commission (“SEC”), news releases, reports, proxy statements, registration statements and other written communications, as well as forward-looking statements made from time to time by representatives of our Company. These risks and uncertainties include those listed in the Company’s Annual Report on Form 10-K for the fiscal year ended September 25, 2011. These risks and uncertainties and additional risks and uncertainties not presently known to us or that we currently deem immaterial may cause our business, financial condition, operating results and cash flows to be materially adversely affected. Except for the historical information contained herein, the matters discussed in this analysis are forward-looking statements that involve risks and uncertainties, including general business conditions, changes in overall economic conditions that impact consumer spending, including fuel prices and housing market trends, the impact of competition and other factors which are often beyond the control of the Company. The Company does not undertake any obligation to update forward-looking statements.

This information should be read in conjunction with the consolidated financial statements and the accompanying notes included in Item 1 of Part I of this Quarterly Report on Form 10-Q and the Company’s Annual Report on Form 10-K for the fiscal year ended September 25, 2011.

General

Whole Foods Market, Inc. is the world’s leading retailer of natural and organic foods and America’s first national “Certified Organic” grocer. Our Company mission is to promote the vitality and well-being of all individuals by supplying the highest quality, most wholesome foods available. Through our growth, we have had a significant and positive impact on the natural and organic foods movement throughout the United States, helping lead the industry to nationwide acceptance. As of April 8, 2012, we operated 320 stores: 307 stores in 38 U.S. states and the District of Columbia; 7 stores in Canada; and 6 stores in the United Kingdom. We have one operating segment, natural and organic foods supermarkets.

Our results of operations may be impacted by the timing of new store openings, construction and pre-opening expense, store closures and relocations, and the range of operating results generated from newly opened stores. The Company’s average weekly sales and gross profit are typically highest in the second and third fiscal quarters, and lowest in the fourth fiscal quarter. Average weekly sales and gross profit are typically lower in the first fiscal quarter due to the product mix of holiday sales, and in the fourth fiscal quarter due to the seasonally slower sales during the summer months.

Sales of a store are deemed to be comparable commencing in the fifty-third full week after the store was opened or acquired. Identical store sales exclude sales from relocated stores and remodeled stores with changes in square footage greater than 20% from the comparable calculation to reduce the impact of square footage growth on the comparison. Stores closed for eight or more days are excluded from the comparable and identical store base from the first fiscal week of closure until re-opened for a full fiscal week.

The Company reports its results of operations on a 52- or 53-week fiscal year ending on the last Sunday in September. Fiscal year 2012 is a 53-week year and fiscal year 2011 was a 52-week year.

Economic and Industry Factors

Food retailing is a large, intensely competitive industry. Our competition varies across the Company and includes but is not limited to local, regional, national and international conventional and specialty supermarkets, natural foods stores, warehouse membership clubs, smaller specialty stores, farmers’ markets, and restaurants, each of which competes with us on the basis of store ambiance and experience, product selection, quality, customer service, price or a combination of these factors. Natural and organic food continues to be one of the fastest growing segments of food retailing today. Our commitment to natural and organic products, high quality standards, emphasis on perishable product sales, healthy eating products and education, range of choices based on price, and empowered team members who focus on unparalleled customer service differentiate us from the competition and have created a loyal customer base.

We have worked very hard over the last couple of years to successfully improve our price image, particularly in perishables, and we are focused on improving our relative price positioning in the marketplace. We are hopeful we can continue to strike the right balance between rising product costs and our retail pricing based on our contracts, distribution, and tools to manage value.

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Highlights for the Second Quarter of Fiscal Year 2012

We are pleased to report another consistently strong quarter, producing the best results in our 32-year history. For the twelve weeks ended April 8, 2012:

• Sales increased 13.6% over the same period of the prior year to $2.67 billion driven by a 9.5% comparable store sales increase. Identical store sales increased 9.0% over the prior year;

• Gross profit as a percentage of sales increased to 36.3%, a new record;

• Operating income as a percentage of sales improved year-over-year for the twelfth consecutive quarter to 7.1%;

• Diluted earnings per share increased 25.5% over the same period of the prior year to $0.64;

• We produced $255.8 million in cash flow from operations and invested $101.9 million in capital expenditures;

• The Company made a dividend payment to shareholders totaling $25.2 million; and

• We had cash, restricted cash and investments totaling $1.30 billion.

Updated Outlook for Fiscal Year 2012

Our exceptional results during the twenty-eight weeks ended April 8, 2012 have given us the confidence to significantly raise our guidance for the full year. We are confident that our sales momentum and operating disciplines will create continued positive results for our shareholders. The following table provides additional information on the Company’s results through April 8, 2012 and expectations for the remainder of fiscal year 2012.

	Twenty-eight weeks ended April 8, 2012	Implied third and fourth quarters of fiscal year 2012	Estimated fiscal year 2012
Sales growth	13.2%	16.7% - 18.2%	14.8% - 15.6%
Comparable store sales growth	9.0%	7.2% - 8.8%	8.2% - 8.9%
Identical store sales growth	8.6%	7.0% - 8.6%	7.8% - 8.6%
General and administrative expenses	3.1%	3.1%	3.1%
Diluted earnings per share	$1.29	$1.15 - $1.18	$2.44 - $2.47
Diluted earnings per share growth	26.9%	25.0% - 28.0%	26.0% - 28.0%

Fiscal year 2012 is a 53-week fiscal year, with the extra week falling in the fourth fiscal quarter. The Company estimates the impact on earnings from the extra week to be $0.06 per share. On a 52-week to 52-week basis, excluding the impact of the extra week in the fourth fiscal quarter, the Company expects total sales growth of 13% and earnings per share growth of 23% to 25%.

The Company continues to expect ending square footage growth of 7% to 8% in fiscal year 2012. The Company expects capital expenditures for fiscal year 2012 to be in the range of approximately $410 million to $460 million, which includes the opening of 24 to 27 new stores.

Results of Operations

The following table sets forth the Company’s statements of operations data expressed as a percentage of sales:

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Sales	100.0	%	100.0	%	100.0	%	100.0	%
Cost of goods sold and occupancy costs	63.7		64.4		64.6		65.0
Gross profit	36.3		35.6		35.4		35.0
Direct store expenses	25.5		25.9		25.6		26.1
General and administrative expenses	3.2		3.2		3.1		3.1
Pre-opening expenses	0.4		0.4		0.3		0.3
Relocation, store closure and lease termination costs	—		—		0.1		0.1
Operating income	7.1		6.0		6.3		5.4
Investment and other income, net of interest	0.1		—		0.1		—
Income before income taxes	7.2		6.1		6.3		5.4
Provision for income taxes	2.8		2.2		2.4		2.1
Net income	4.4	%	3.8	%	3.9	%	3.3	%

Figures may not sum due to rounding.

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Sales for the twelve and twenty-eight weeks ended April 8, 2012 totaled approximately $2.67 billion and $6.06 billion, respectively, increasing 13.6% and 13.2%, respectively, over the same periods of the prior fiscal year. Comparable store sales increased 9.5% and 9.0% during the twelve and twenty-eight weeks ended April 8, 2012, respectively. As of April 8, 2012, there were 304 locations in the comparable store base. Identical store sales, excluding six relocations and two expansions, increased 9.0% during the twelve weeks ended April 8, 2012. During the twenty-eight weeks ended April 8, 2012, identical store sales increased 8.6% and excluded six relocations and three expansions. Relocations and expansions are removed from the comparable calculation to reduce the impact of square footage growth on the comparison. Comparable and identical store sales for the twelve and twenty-eight weeks ended April 8, 2012 include a positive impact of 55 basis points and 25 basis points, respectively, resulting from the shift of Easter from the third fiscal quarter of the prior year to the second fiscal quarter of the current year. At April 8, 2012, there were 21 stores that were opened or acquired fifty-two weeks or less which contributed approximately $128.8 million and $275.6 million to total sales during the twelve and twenty-eight weeks ended April 8, 2012, respectively. During the twelve weeks ended April 8, 2012, our transaction count in identical stores accelerated to 7.3% and our sales momentum continues to be broad-based across regions, departments, and store age classes.

The Company’s gross profit as a percentage of sales for the twelve and twenty-eight weeks ended April 8, 2012 was approximately 36.3% and 35.4%, respectively, compared to approximately 35.6% and 35.0%, respectively, for the same periods of the prior fiscal year. Gross margin increased70 basis points and 41 basis points for the twelve and twenty-eight weeks ended April 8, 2012, respectively, compared to the same periods of the prior fiscal year. The increase in gross profit as a percentage of sales for the twelve weeks ended April 8, 2012 was driven by equal improvements in occupancy costs and cost of goods sold as a percentage of sales, while the increase in the twenty-eight weeks ended April 8, 2012 was primarily driven by occupancy costs. Occupancy costs continue to be leveraged through strong disciplines through lease negotiation and were benefited by a milder winter through much of the United States during the second fiscal quarter. Improved cost of goods sold during the twelve weeks ended April 8, 2012 reflect a focus on stronger buying and inventory management, including better shrink control and lower days inventory is on hand. While we are very proud to have produced record margin results during the twelve weeks ended April 8, 2012, our longer term strategy has not changed, and while we have confidence that we can continue to deliver excellent results, our goal remains to consistently deliver gross profit on an annual basis within our historical range of 34% to 35%.

Direct store expenses as a percentage of sales for the twelve and twenty-eight weeks ended April 8, 2012 were approximately 25.5% and 25.6%, respectively, compared to approximately 25.9% and 26.1%, respectively, for the same periods of the prior fiscal year. The 37 basis point and 52 basis point decrease in direct store expenses as a percentage of sales for the twelve and twenty-eight weeks ended April 8, 2012, respectively, primarily reflects leverage in wages and depreciation expense.

General and administrative expenses as a percentage of sales were consistent for the twelve and twenty-eight weeks ended April 8, 2012 compared to the same periods of the prior fiscal year at approximately 3.2% and 3.1%, respectively.

Pre-opening expenses totaled approximately $10.5 million and $20.9 million for the twelve and twenty-eight weeks ended April 8, 2012, respectively, and approximately $9.5 million and $18.2 million, respectively, the same periods of the prior fiscal year.

Relocation, store closure and lease termination costs totaled approximately $1.3 million and $4.2 million for the twelve and twenty-eight weeks ended April 8, 2012, respectively, compared to approximately $1.0 million and $4.1 million, respectively, for the same periods of the prior fiscal year.

The numbers of stores opened and relocated were as follows:

	Twelve weeks ended		Twenty-eight weeks ended
	April 8, 2012	April 10, 2011	April 8, 2012	April 10, 2011
New stores	3	2	9	5
Relocated stores	—	1	—	1

Investment and other income, net of interest expense, which includes interest income, investment gains and losses, rental income and other income, totaled approximately $2.3 million and $4.6 million for the twelve and twenty-eight weeks ended April 8, 2012, respectively, compared to approximately $0.7 million and $1.0 million, respectively, for the same periods of the prior fiscal year. The increase is primarily related to a reduction in interest expense due to the repayment of our term loan in fiscal year 2011.

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Income taxes for the twelve and twenty-eight weeks ended April 8, 2012 resulted in an effective tax rate of approximately 38.6% compared to approximately 37.0% and 38.5%, respectively, for the same periods of the prior fiscal year.

Share-based payment expense was included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended						Twenty-eight weeks ended
	April 8, 2012			April 10, 2011			April 8, 2012			April 10, 2011
Cost of goods sold and occupancy costs	$	372		$	288		$	945		$	658
Direct store expenses	4,473			2,894			10,363			6,619
General and administrative expenses	3,697			2,307			8,451			5,571
Share-based payment expense before income taxes	8,542			5,489			19,759			12,848
Income tax benefit	(3,236		)	(1,999		)	(7,454		)	(4,870		)
Net share-based payment expense	$	5,306		$	3,490		$	12,305		$	7,978

Liquidity and Capital Resources and Changes in Financial Condition

The following table summarizes the Company’s cash and short-term investments as of the dates indicated (in thousands):

	April 8, 2012		September 25, 2011
Cash and cash equivalents	$	175,375	$	212,004
Short-term investments - available-for-sale securities	881,945		442,320
Restricted cash	104,942		91,956
Total	$	1,162,262	$	746,280

Additionally, the Company had long-term investments in available-for-sale securities totaling approximately $140.0 million and $52.8 million at April 8, 2012 and September 25, 2011, respectively.

We generated cash flows from operating activities totaling approximately $516.7 million during the twenty-eight weeks ended April 8, 2012 compared to approximately $402.8 million during the same period of the prior fiscal year. Cash flows from operating activities resulted primarily from our net income plus non-cash expenses and changes in operating working capital.

Net cash used in investing activities totaled approximately $760.0 million for the twenty-eight weeks ended April 8, 2012 compared to approximately $220.0 million for the same period of the prior fiscal year. Net purchases of available-for-sale securities totaled approximately $532.2 million during the twenty-eight weeks ended April 8, 2012 compared to approximately $48.8 million in the same period of the prior fiscal year. Our principal historical capital requirements have been the funding of the development or acquisition of new stores and acquisition of property and equipment for existing stores. The required cash investment for new stores varies depending on the size of the new store, geographic location, degree of work performed by the landlord and complexity of site development issues. Capital expenditures for the twenty-eight weeks ended April 8, 2012 totaled approximately $213.3 million, of which approximately $114.5 million was for new store development and approximately $98.7 million was for remodels and other additions. Capital expenditures for the twenty-eight weeks ended April 10, 2011 totaled approximately $169.6 million, of which approximately $89.5 million was for new store development and approximately $80.1 million was for remodels and other additions.

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The following table provides information about the Company’s store development activities:

	Stores opened during fiscal year 2011	Stores opened during fiscal year 2012	Properties tendered as of May 2, 2012	Total leases signed as of May 2, 2012 (1)
Number of stores (including relocations)	18	13	18	70
Number of relocations	6	—	3	9
New markets	—	4	7	21
Average store size (gross square feet)	39,400	34,900	34,000	35,400
Total square footage	708,700	454,200	612,700	2,499,500
Average tender period in months	12.5	7.5
Average pre-opening expense per store	$2.5 million
Average pre-opening rent per store	$1.2 million

⁽¹⁾ Includes leases for properties tendered

The Company expects to open 15 to 18 additional stores, including one to two relocations, during the remainder of fiscal year 2012. We believe we will produce operating cash flows in excess of the capital expenditures needed to open the 70 stores in our store development pipeline. The following table provides information about the Company’s estimated store openings for the next two fiscal years:

	Estimated openings	Relocations	Average new store square footage	Ending square footage growth
Fiscal year 2012	24 - 27	1 - 2	35,000	7% - 8%
Fiscal year 2013	28 - 32	2 - 3	35,000	7% - 8%

Over the long term, the Company considers 1,000 stores to be a reasonable indication of its market opportunity in the United States as the Whole Foods Market brand continues to strengthen, consumer demand for natural and organic products continues to increase, and the Company’s flexibility on new store size opens up additional market opportunities. The Company believes significant opportunities exist in Canada and the United Kingdom as well.

Net cash provided by financing activities was approximately $205.7 million for the twenty-eight weeks ended April 8, 2012 compared to net cash used in financing activities of approximately $155.2 million for the same period of the prior fiscal year.

Net proceeds to the Company from team members’ stock plans for the twenty-eight weeks ended April 8, 2012 totaled approximately $237.0 million compared to approximately $153.1 million for the same period of the prior fiscal year. The Company intends to keep its broad-based stock option program in place, but also intends to limit the number of shares granted in any one year so that annual earnings dilution from share-based payment expense will not exceed 10%. The Company believes this strategy is best aligned with its stakeholder philosophy because it limits future earnings dilution from options and at the same time retains the broad-based stock option plan, which the Company believes is important to team member morale, its unique corporate culture and its success. At April 8, 2012 and September 25, 2011, approximately 11.8 million shares and 11.7 million shares of our common stock, respectively, were available for future stock incentive grants.

18

During the first quarter of fiscal year 2012, the Company’s Board of Directors announced a 40% increase in the quarterly dividend to $0.14 per common share. Following is a summary of dividends declared per common share during fiscal years 2012 and 2011 (in thousands, except per share amounts):

Date of declaration	Dividend per common share		Date of record	Date of payment	Total amount
Fiscal year 2012:
November 2, 2011	$	0.14	January 13, 2012	January 24, 2012	$	25,230
March 9, 2012 (1)	0.14		April 5, 2012	April 17, 2012	25,610
Fiscal year 2011:
December 8, 2010	$	0.10	January 10, 2011	January 20, 2011	$	17,348
February 27, 2011	0.10		April 12, 2011	April 22, 2011	17,572
June 7, 2011	0.10		June 24, 2011	July 5, 2011	17,700
September 8, 2011	0.10		September 19, 2011	September 29, 2011	17,827

⁽¹⁾ Dividend accrued at April 8, 2012

The Company will pay future dividends at the discretion of the Board of Directors. The continuation of these payments, the amount of such dividends, and the form in which dividends are paid (cash or stock) depend on many factors, including the results of operations and the financial condition of the Company. Subject to these qualifications, the Company currently expects to pay dividends on a quarterly basis.

During the first quarter of fiscal year 2012, the Company’s Board of Directors authorized a share repurchase program in the amount of $200 million through November 1, 2013. During the first quarter of fiscal year 2012, the Company repurchased 56,500 shares of Company common stock on the open market for a total of approximately $3.6 million. No additional repurchases of shares was made during the twelve weeks ended April 8, 2012, however we have committed to additional share repurchases through the remainder of fiscal year 2012. The specific timing and repurchase of future amounts will vary based on market conditions, securities law limitations, and other factors and will be made using the Company’s available resources. The repurchase program may be suspended or discontinued at any time at the Company’s discretion.

The Company has a $350 million revolving line of credit that extends to August 28, 2012. The Company’s obligations under the facility are secured by liens on certain of the Company’s assets, including stock of its subsidiaries. The credit agreement contains certain affirmative covenants including maintenance of certain financial ratios and certain negative covenants including limitations on additional indebtedness and payments as defined by the agreement. At April 8, 2012 the Company was in compliance with all applicable debt covenants. At April 8, 2012 and September 25, 2011 the Company had no amounts drawn under this agreement. The amount available to the Company under the agreement was $350 million at April 8, 2012. The amount available to the Company at September 25, 2011 was effectively reduced to approximately $348.6 million by outstanding letters of credit totaling approximately $1.4 million. The Company had outstanding a $700 million, five-year term loan agreement due in 2012, with an outstanding balance of $490 million at September 26, 2010. During the twenty-eight weeks ended April 10, 2011, the Company repaid $300 million on the term loan and repaid the remainder throughout fiscal year 2011.

The Company is committed under certain capital leases for rental of certain equipment, buildings and land, and certain operating leases for rental of facilities and equipment. These leases expire or become subject to renewal clauses at various dates through 2054.

The following table shows payments due by period on contractual obligations as of April 8, 2012 (in thousands):

	Total		Less than 1 year		1-3 years		3-5 years		More than 5 years
Capital lease obligations (including interest)	$	39,617	$	2,104	$	4,250	$	4,125	$	29,138
Operating lease obligations (1)	6,298,605		310,126		708,653		736,551		4,543,275
Total	$	6,338,222	$	312,230	$	712,903	$	740,676	$	4,572,413

⁽¹⁾ Amounts exclude taxes, insurance and other related expense

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Gross unrecognized tax benefits and related interest and penalties at April 8, 2012 were approximately$10.5 million. Although a reasonably reliable estimate of the period of cash settlement with respective taxing authorities cannot be determined due to the high degree of uncertainty regarding the timing of future cash outflows associated with the Company’s unrecognized tax benefits, as of April 8, 2012, the Company does not expect tax audit resolution will reduce its unrecognized tax benefits in the next 12 months.

We periodically make other commitments and become subject to other contractual obligations that we believe to be routine in nature and incidental to the operation of the business. Management believes that such routine commitments and contractual obligations do not have a material impact on our business, financial condition or results of operations.

The effect of exchange rate changes on cash included in the Consolidated Statements of Cash Flows resulted in an increase in cash and cash equivalents totaling approximately $1.0 million for the twenty-eight weeks ended April 8, 2012 compared to an increase of approximately $2.4 million for the same period of the prior fiscal year. These changes principally reflect the relative strengthening of the Canadian dollar and pound sterling compared to the U.S. dollar during these periods.

Our principal historical sources of liquidity have been cash generated by operations, available cash and cash equivalents, short-term investments, and amounts available under our revolving line of credit. Absent any significant change in market condition, we expect planned expansion and other anticipated working capital and capital expenditure requirements for the next twelve months will be funded by these sources. There can be no assurance, however, that the Company will continue to generate cash flows at or above current levels or that our revolving line of credit and other sources of capital will be available to us in the future.

Off-Balance Sheet Arrangements

Our off-balance sheet arrangements at April 8, 2012 consist of operating leases disclosed in the above contractual obligations table and outstanding letters of credit discussed in Note 7 to the consolidated financial statements, “Long-Term Debt.” We have no other off-balance sheet arrangements that have had, or are reasonably likely to have, a material current or future effect on our consolidated financial statements or financial condition.

Recent Accounting Pronouncements

Recent accounting pronouncements are included in Note 2 to the consolidated financial statements, “Recent Accounting Pronouncements.”

Item 4. Controls and Procedures

The Company maintains disclosure controls and procedures that are designed to ensure that information required to be disclosed by us in the reports we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the Securities and Exchange Commission’s rules and forms, and that such information is accumulated and communicated to our management, including our Co-Chief Executive Officers (principal executive officers) and Chief Financial Officer (principal financial officer), to allow timely decisions regarding required disclosure. The Company’s management, with the participation of the Company’s Co-Chief Executive Officers and Chief Financial Officer, has evaluated the effectiveness of the Company’s disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) as of the end of the period covered by this report. Based on such evaluation, the Company’s Co-Chief Executive Officers and Chief Financial Officer have concluded that, as of the end of such period, the Company’s disclosure controls and procedures were effective as of the end of the period covered by this report.

There have been no changes in the Company’s internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during the most recent fiscal quarter that have materially affected, or are reasonably likely to materially affect, the Company’s internal control over financial reporting.

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Part II. Other Information

Item 1. Legal Proceedings

The Company is exposed to claims and litigation matters arising in the ordinary course of business and uses various methods to resolve these matters in a manner that we believe best serves the interests of our stakeholders. We have exposures to loss contingencies arising from pending or threatened litigation for which assessing and estimating the outcomes of these matters involve substantial uncertainties.

On October 27, 2008, Whole Foods Market was served with the complaint in Kottaras v. Whole Foods Market, Inc., a putative class action filed in the United States District Court for the District of Columbia, seeking treble damages, equitable, injunctive, and declaratory relief and alleging that the acquisition and merger between Whole Foods Market and Wild Oats violates various provisions of the federal antitrust laws. During first quarter of fiscal year 2012, the federal district judge denied the plaintiff’s motion for class certification. Currently that decision is being appealed. The Company has not accrued any loss related to the outcome of this case as of April 8, 2012.

The Company evaluates contingencies on an ongoing basis and has established loss provisions for matters in which losses are probable and the amount of loss can be reasonably estimated. Legal settlement liabilities are included in the “Other current liabilities” line item on the Consolidated Balance Sheets. We believe the recorded reserves in our consolidated financial statements are adequate in light of the probable and estimable liabilities. However, resolution of contingencies resulting in amounts that vary materially from the Company’s current estimates could have a material adverse effect on the Company’s results of operations, cash flows, or financial condition.

Item 5. Other Information

Amendment to Whole Foods Executive Retention Plan and Non-Compete Arrangement

Plan Description and 2010 Agreements

During fiscal year 2010, the Company entered into agreements (the “2010 Agreements”) pursuant to its Executive Retention Plan and Non-Compete Arrangement (the “Plan”) with certain members of the Company’s management. In keeping with his voluntary decision in 2007 to reduce his annual salary to $1 and forgo earning any future cash compensation, stock awards and options awards, John Mackey, Co-Chief Executive Officer, opted not to execute such agreement.

Pursuant to the Plan and the 2010 Agreements, if a covered person’s employment is terminated (a) by the Company other than for “cause” (as defined in the Plan) or (b) by the covered person, and, within 45 days of termination, the covered person signs a release, then, subject to the covered person’s continued compliance with the confidentiality, non-compete, non-solicitation, non-disparagement and other restrictions of the Plan, the covered person will receive certain non-compete benefits from the Company, including: (i) immediate vesting of all restricted stock, stock options and other similar awards and (ii) up to a designated non-compete payment for a maximum of five years, paid in equal, semiannual installments; provided, that if the covered person voluntarily terminates employment for a reason other than “good reason” (as defined in the Plan), “disability” (as defined in the Plan) or death, then, unless the covered person has held his or her current position or one of several other designated positions with the Company for 15 years or more, such payment will be reduced by 20% for each year below 15 years of employment in a designated position.

Additionally, for the two-year period following a change of control, the Plan and 2010 Agreements provide the covered person with guaranteed compensation and participation in benefit plans and, if the covered person is terminated other than for “cause” (as defined in the Plan) or terminates employment with “good reason” (as defined in the Plan) during that period, a lump sum payment equal to three times the covered person’s annual compensation.

The 2010 Agreements with Walter Robb, A.C. Gallo, Glenda Flanagan and Jim Sud also provide that if the covered person voluntarily terminates employment for a reason other than a “good reason” (as defined in the Plan), “disability” (as defined in the Plan) or death, the non-compete benefits described two paragraphs above shall not be automatically set, but instead are subject to future negotiation.

21

Amendments to Plan and 2010 Agreements / Promotions of New Executive Vice Presidents

On May 16, 2012, the Board of Directors approved the following amendments to the Plan and the 2010 Agreements with Walter Robb, A.C. Gallo, Glenda Flanagan and Jim Sud to provide: (i) the minimum non-compete payment that may be negotiated following a voluntary termination is a percentage of the maximum non-compete payment (that percentage is 0% until October 1, 2012, becomes 20% on October 1, 2012, and increases by an additional 20% on each anniversary of October 1, 2012 until October 1, 2016) and (ii) the maximum potential non-compete payment would not be reduced based on the length of time the person has been in his or her current position or another designated position.

On May 16, 2012, the Board of Directors also approved amendments to the 2010 Agreements with David Lannon and Ken Meyer, based on their recent promotions, (the “Promotion Agreements”) to increase the amount of the maximum semi-annual non-compete payment for each of them to $400,000, adjusted to reflect the increase, if any, in the Consumer Price Index. To make the Promotion Agreements consistent with the 2010 Agreements of our other Executive Team Members, the Promotion Agreements also include the provisions described in the preceding paragraph and provide that if the covered person voluntarily terminates employment for a reason other than a “good reason” (as defined in the Plan), “disability” (as defined in the Plan) or death, the non-compete benefits shall not be automatically set, but instead are subject to future negotiation.

Item 6. Exhibits

Exhibit   3.1	Amended and Restated Articles of Incorporation of the Registrant, dated March 9, 2012
Exhibit  31.1	Certification of Co-Chief Executive Officer Pursuant to 17 CFR 240.13a -14(a)
Exhibit  31.2	Certification of Co-Chief Executive Officer Pursuant to 17 CFR 240.13a - 14(a)
Exhibit  31.3	Certification of Chief Financial Officer Pursuant to 17 CFR 240.13a - 14(a)
Exhibit  32.1	Certification of Co-Chief Executive Officer Pursuant to 18 U.S.C. Section 1350
Exhibit  32.2	Certification of Co-Chief Executive Officer Pursuant to 18 U.S.C. Section 1350
Exhibit  32.3	Certification of Chief Financial Officer Pursuant to 18 U.S.C. Section 1350
Exhibit  101	The following financial information from the Company’s Quarterly Report on Form 10-Q, for the period ended April 8, 2012, formatted in eXtensible Business Reporting Language: (i) Consolidated Balance Sheets, (ii) Consolidated Statements of Operations, (iii) Consolidated Statements of Shareholders’ Equity, (iv) Consolidated Statements of Cash Flows, (v) Notes to Consolidated Financial Statements (1)

(1) Pursuant to Rule 406T of Regulation S-T, the Interactive Data Files hereto are deemed not filed or part of a registration statement or prospectus for purposes of Sections 11 or 12 of the Securities Act of 1933, as amended, are deemed not filed for purposes of Section 18 of the Securities and Exchange Act of 1934, as amended, and otherwise are not subject to liability under those sections.

22

SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

		WHOLE FOODS MARKET, INC.
Date:	May 17, 2012	By:	/s/ Glenda Flanagan
		Glenda Flanagan
		Executive Vice President and Chief Financial Officer
		(Duly authorized officer and principal financial officer)

23

EX-3.1

Corporations Section P.O.Box 13697 Austin, Texas 78711-3697		Hope Andrade
		Secretary of State

Office of the Secretary of State

CERTIFICATE OF FILING

OF

WHOLE FOODS MARKET, INC.

44435900

The undersigned, as Secretary of State of Texas, hereby certifies that a Certificate of Amendment for the above named entity has been received in this office and has been found to conform to the applicable provisions of law.

ACCORDINGLY, the undersigned, as Secretary of State, and by virtue of the authority vested in the secretary by law, hereby issues this certificate evidencing filing effective on the date shown below.

Dated: 03/09/2012

Effective: 03/09/2012

	/s/ Hope Andrade
	Hope Andrade Secretary of State

Come visit us on the internet at http://www.sos.state.tx.us/
Phone: (512)463-5555	Fax: (512) 463-5709	Dial: 7-1-1 for Relay Services
Prepared by: Lynda Boots	TID: 10303	Document: 412150920002

CERTIFICAT OF AMENDMENT

OF

WHOLE FOODS MARKET, INC.

A Texas Corporation

Whole Foods Market, Inc., a Texas for-profit corporation (the "Corporation"), hereby adopts this Certificate of Amendment (the "Amendment").

1. The name of the Corporation is Whole Foods Market, Inc.

2. The file number issued to the Corporation by the secretary of state is 44435900.

3. The date of formation of the Corporation is August 15, 1978.

4. The following identified provision is amended as follows:

The second sentence of ARTICLE IV, Section A is replaced with the following sentence:

"The aggregate number of shares of Common Stock authorized to be issued is 600,000,000 shares with no par value."

5. This Amendment has been approved in the manner required by the Texas Business Organizations. Code and by the governing documents of the Corporation.

6. This document becomes effective when the document is filed by the secretary of state.

[Reminder of page intentionally left blank]

The undersigned signs this document subject to the penalties imposed by law for the submission of a materially false or fraudulent instrument and certifies under penalty of perjury that the undersigned is authorized under the provisions of law governing the entity to execute the filing instrument.

Date: March 9, 2012

WHOLE FOODS MARKET, INC
a Texas corporation
By:	/s/Glenda Flanagan
	Glenda Flanagan
	Chief Financial Officer

	Office of the Secretary of State	Filed in the Office of the
	Corporations Section	Secretary of State of Texas
	P.O. Box 13697	Filing #: 44435900 04/19/2010
	Austin, Texas 78711-3697	Document #: 304538400461
	(Form 408)	Image Generated Electronically

STATEMENT OF CHANGE OF

ADDRESS OF REGISTERED AGENT

1. The name of the entity represented is

WHOLE FOODS MARKET, INC.

The entity's filing number is 44435900

2. The address at which the registered agent has maintained the registered office address for such entity is: (Please provide street address, city, state and zip code presently shown in the records of the Secretary of State.)

350 N. St. Paul St., Dallas, TX 75201

3. The address at which the registered agent will hereafter maintain the registered office address for such entity is: (Please provide street address, city, state and zip code. The address must be in Texas.)

350 N. St. Paul St., Ste. 2900, Dallas, TX 75201-4234

4. Notice of the change of address has been given to said entity in writing at least 10 business days prior to the submission of this filing.

Date: 04/19/2010

CT Corporation System

Name of Registered Agent

Kenneth Uva, Vice President

Signature of Registered Agent

FILING OFFICE COPY

Corporations Section P.O.Box 13697 Austin, Texas 78711-3697		Roger Williams
		Secretary of State

Office of the Secretary of State

CERTIFICATE OF RESTATED ARTICLES

OF

WHOLE FOODS MARKET, INC.

44435900

The undersigned, as Secretary of State of Texas, hereby certifies that the Restated Articles for the above named entity have been received in this office and have been found to conform to law.

ACCORDINGLY the undersigned, as Secretary of State, and by virtue of the authority vested in the Secretary by law hereby issues this Certificate of Restated Articles.

Dated: 03/24/2006

Effective: 03/24/2006

	/s/ Roger Williams
	Roger Williams Secretary of State

Come visit us on the internet at http://www.sos.state.tx.us/
Phone: (512)463-5555	Fax: (512) 463-5709	Dial: 7-1-1
Prepared by: Delores Eitt		Document: 122343810002

AMENDED AND RESTATED

ARTICLES OF INCORPORATION

(With Amendments)

OF

WHOLEFOODS MARKET,INC.

A Texas Corporation

Pursuant to the provisions of the Texas Business Corporation Act, Whole Foods Market, Inc., a Texas corporation (the "Corporation"), hereby adopts these Amended and Restated Articles of Incorporation (the "Restated Articles"), which accurately reflect the original Articles of Incorporation and all amendments thereto that are in effect to date (collectively, the "Original Articles") and as further amended by such Restated Articles as hereinafter set forth and which contain no other change in any provision thereof.

1.     The name of the Corporation is Whole Foods Market, Inc.

2.     The Original Articles of the Corporation are amended by these Restated Articles as follows:

ARTICLE VI is amended and restated in its entirety to read as set forth in ARTICLE VI of the Restated Articles by adding a paragraph to provide for majority shareholder voting on all matters for which the Texas Business Corporation Act would otherwise specify a higher required percentage.

3.        These Restated Articles have been effected in conformity with the provisions of the Texas Business Corporation Act and the Corporation's constituent documents, and these Restated Articles and each such amendment made by these Restated Articles were duly adopted and approved by the shareholders of the Corporation as of March 6, 2006.

4.        The Original Articles are hereby superseded by the following Restated Articles, which accurately copy the entire text thereof as amended as set forth above:

[Reminder of page intentionally left blank]

AMENDED AND RESTATED

ARTICLES OF INCORPORATION

OF

WHOLE FOODS MARKET,INC.

A Texas Corporation

ARTICLE I

The name of the Corporation is Whole Foods Market, Inc.

ARTICLE II

The period of its duration is perpetual.

ARTICLE III

The purpose or purposes for which the Corporation is organized are to transact any and all lawful business for which businesses may be incorporated under the Texas Business Corporation Act.

ARTICLE IV

A. The Corporation is authorized to issue two classes of shares of capital stock, designated "Common Stock" and "Preferred Stock," respectively. The aggregate number of shares of Common Stock authorized to be issued is 300,000,000 shares with no par value. The aggregate number of shares of Preferred Stock authorized to be issued is 5,000,000 shares with a par value of $.01 per share. Shares of the Preferred Stock maybe issued from time to time in one or more series, each such series to have such distinctive designation or title as may be fixed by the Board of Directors prior to the issuance of any shares thereof. Each such series shall have such designations, preferences, limitations and relative rights, including voting rights, as shall be stated in the resolution or resolutions providing for the issuance of such series of Preferred Stock, as may be adopted from time to time by the Board of Directors prior to the issuance of any shares thereof, in accordance with the laws of the State of Texas. The Board of Directors, in such resolution or resolutions, may increase or decrease the number of shares within each such series; provided, however, the Board of Directors may not decrease the number of shares within a series to less than the number of shares within such series that are then issued.

B. No shareholder of the Corporation will, by reason of his holding shares of stock of the Corporation, have any preemptive or preferential rights to purchase or subscribe to any shares of any class of stock of the Corporation, or any notes, debentures, bonds,

warrants, options or other securities of the Corporation, whether now or hereafter authorized.

ARTICLE V

Cumulative voting in the election of directors is prohibited.

ARTICLE VI

Any action required by the Texas Business Corporation Act to be taken at any annual or special meeting of the shareholders, or any action which may be taken at any annual or special meeting of shareholders, may be taken without a meeting, without prior notice and without a vote if a consent or consents in writing, setting forth the action so taken, shall be signed by the holder or holders of shares having not less than the minimum number of votes that would be necessary to take such action at a meeting at which the holders of all shares entitled to vote on the action were present and voted.

If, with respect to any action taken by the shareholders of the corporation, any provision of the Texas Business Corporation Act would, but for this Article VI, require the vote or concurrence of the holders of shares having more than a majority of the votes entitled to be cast thereon, or of any class or series thereof, the vote or concurrence of the holders of shares having only a majority of the votes entitled to be cast thereon, or of any class or series thereof, shall be required with respect to any such action.

ARTICLE VII

The Corporation will not commence business until it has received for the issuance of its shares consideration of the value of not less than One Thousand Dollars ($1,000), consisting of money, labor done, or property actually received.

ARTICLE VIII

The address of the Corporation's registered office is 1021 Main Street, Suite 1150, Houston, TX 77002, and the name of its registered agent at such address is CT Corporation System.

ARTICLE IX

No director of the Corporation shall be liable to the Corporation or its shareholders for an act or omission in such capacity as a director except liability resulting from:

1. A breach of the director's duty of loyalty to the Corporation or its shareholders;

2. An act or omission not in good faith that involves intentional misconduct or a knowing violation of the law;

3. A transaction from which the director receives an improper benefit, whether or not the

benefit resulted from an action taken within the scope of the director's office;

4. An act or omission for which the liability of the director is expressly provided for by a statute; or

5. An act related to an unlawful stock repurchase or payment of a dividend.

ARTICLE X

The number of directors constituting the Board of Directors shall be provided for in the bylaws of the Corporation. The names and addresses of the persons who are now serving as directors of the Corporation are:

NAME	ADDRESS
John P. Mackey	550 Bowie Street
	Austin, TX 78703
David W. Dupree	550 Bowie Street
	Austin, TX 78703
Dr. John B. Elstrott	550 Bowie Street
	Austin, TX 78703
Linda A. Mason	550 Bowie Street
	Austin, TX 78703
Gabrielle E. Greene	550 Bowie Street
	Austin, TX 78703
Morris J. Siegel	550 Bowie Street
	Austin, TX 78703
Dr. Ralph Z. Sorenson	550 Bowie Street
	Austin, TX 78703
Hass Hassan	550 Bowie Street
	Austin, TX 78703

ARTICLE XI

The Corporation shall, to the full extent permitted by applicable law, indemnify any person who was or is a party or is threatened to be made a party to any threatened, pending or contemplated action, suit or proceeding by reason of the fact that such person is or was an officer or director of the Corporation.

[Signature Page Follows}

EXECUTED this 24^thdayof March, 2006.

WHOLE FOODS MARKET, INC
a Texas corporation
By:	/s/Glenda Chamberlain
	Glenda Chamberlain
	Executive Vice President

EX-31.1

Exhibit 31.1

CERTIFICATIONS

I, John Mackey, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q of Whole Foods Market, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date:	May 17, 2012
/s/John Mackey
John Mackey
Co-Chief Executive Officer

EX-31.2

Exhibit 31.2

CERTIFICATIONS

I, Walter Robb, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q of Whole Foods Market, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date:	May 17, 2012
/s/Walter Robb
Walter Robb
Co-Chief Executive Officer

EX-31.3

Exhibit 31.3

CERTIFICATIONS

I, Glenda Flanagan, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q of Whole Foods Market, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date:	May 17, 2012
/s/Glenda Flanagan
Glenda Flanagan
Chief Financial Officer

EX-32.1

Exhibit 32.1

Certification by Co-Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes - Oxley Act of 2002

In connection with the Quarterly Report on Form 10-Q of Whole Foods Market, Inc. (the “Company”) for the period ending April 8, 2012 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, John Mackey, Co-Chief Executive Officer of the Company, certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, that:

(1) The Report fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o (d)); and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and result of operations of the Company.

/s/John Mackey

John Mackey

Co-Chief Executive Officer

May 17, 2012

EX-32.2

Exhibit 32.2

Certification by Co-Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes - Oxley Act of 2002

In connection with the Quarterly Report on Form 10-Q of Whole Foods Market, Inc. (the “Company”) for the period ending April 8, 2012 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Walter Robb, Co-Chief Executive Officer of the Company, certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, that:

(1) The Report fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o (d)); and

(2) The information contained in the Report fairly presents, in all material respects, the financial condition and result of operations of the Company.

/s/Walter Robb

Walter Robb

Co-Chief Executive Officer

May 17, 2012

EX-32.3

Exhibit 32.3

Certification by Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the

Sarbanes - Oxley Act of 2002

In connection with the Quarterly Report on Form 10-Q of Whole Foods Market, Inc. (the “Company”) for the period ending April 8, 2012 as filed with the Securities and Exchange Commission on the date hereof (the “Report”), I, Glenda Flanagan, Chief Financial Officer of the Company, certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, that:

(1)The Report fully complies with the requirements of section 13(a) or 15(d) of the Securities Exchange Act of 1934 (15 U.S.C. 78m or 78o (d)); and

(2)The information contained in the Report fairly presents, in all material respects, the financial condition and result of operations of the Company.

/s/Glenda Flanagan

Glenda Flanagan

Chief Financial Officer

May 17, 2012

XML

Reserves for Closed Properties (Details) (USD $)	6 Months Ended	12 Months Ended
	Apr. 08, 2012	Sep. 25, 2011
Restructuring Reserve
Beginning balance	$ 44,702,000	$ 59,298,000
Additions	1,964,000	4,706,000
Usage	(5,154,000)	(17,805,000)
Adjustments	1,203,000	(1,497,000)
Ending Balance	42,715,000	44,702,000
Usage in store closure reserve - ongoing cash rental payments	5,200,000	10,100,000
Usage in store closure reserve - termination fees		7,700,000
Reserve adjustments offset to goodwill		$ 3,700,000

XML

Share-Based Payments (Details 2) (USD $) In Millions, unless otherwise specified	6 Months Ended
	Apr. 08, 2012 Years	Sep. 25, 2011
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Common stock available for future stock option grants (in shares)	11.8	11.7
Unrecognized share-based payment expense, net of estimated forfeitures	$ 75.1	$ 97.4
Nonvested outstanding stock options (in shares)	6.4	6.5
Weighted average period for recognition of unrecognized share-based payment expense (in years)	3

XML

Fair Value Measurements (Details) (Fair value, Measurements, Recurring [Member], USD $) In Thousands, unless otherwise specified	Apr. 08, 2012	Sep. 25, 2011
Level 1 Inputs
Assets, Fair Value Disclosure [Abstract]
Total	$ 125,020	$ 151,113
Level 2 Inputs
Assets, Fair Value Disclosure [Abstract]
Total	1,030,312	511,924
Total
Assets, Fair Value Disclosure [Abstract]
Total	1,155,332	663,037
Money Market Funds [Member] | Level 1 Inputs
Assets, Fair Value Disclosure [Abstract]
Cash Equivalents	20,078	59,157
Restricted Cash	104,942	91,956
Money Market Funds [Member] | Total
Assets, Fair Value Disclosure [Abstract]
Cash Equivalents	20,078	59,157
Restricted Cash	104,942	91,956
Municipal Notes Bonds [Member] | Level 2 Inputs
Assets, Fair Value Disclosure [Abstract]
Cash Equivalents	8,411	3,791
Marketable securities - available-for-sale	458,317	316,662
Municipal Notes Bonds [Member] | Total
Assets, Fair Value Disclosure [Abstract]
Cash Equivalents	8,411	3,791
Marketable securities - available-for-sale	458,317	316,662
Commercial Paper [Member] | Level 2 Inputs
Assets, Fair Value Disclosure [Abstract]
Cash Equivalents		12,998
Marketable securities - available-for-sale	22,985	67,964
Commercial Paper [Member] | Total
Assets, Fair Value Disclosure [Abstract]
Cash Equivalents		12,998
Marketable securities - available-for-sale	22,985	67,964
Corporate Bond Securities [Member] | Level 2 Inputs
Assets, Fair Value Disclosure [Abstract]
Marketable securities - available-for-sale	5,309	5,361
Corporate Bond Securities [Member] | Total
Assets, Fair Value Disclosure [Abstract]
Marketable securities - available-for-sale	5,309	5,361
Variable Rate Demand Obligation [Member] | Level 2 Inputs
Assets, Fair Value Disclosure [Abstract]
Marketable securities - available-for-sale	535,290	105,148
Variable Rate Demand Obligation [Member] | Total
Assets, Fair Value Disclosure [Abstract]
Marketable securities - available-for-sale	$ 535,290	$ 105,148

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Intangible Assets (Tables)

6 Months Ended

Apr. 08, 2012

Intangible Assets, Net (Excluding Goodwill) [Abstract]

Components of intangible assets

The components of intangible assets were as follows (in thousands):

	April 8, 2012					September 25, 2011
	Gross carrying amount		Accumulated amortization			Gross carrying amount		Accumulated amortization
Definite-lived contract-based	$	96,758	$	(33,290	)	$	96,019	$	(31,660	)
Definite-lived marketing-related and other	1,547		(1,019		)	1,547		(420		)
Indefinite-lived contract-based	2,051					1,748
	$	100,356	$	(34,309	)	$	99,314	$	(32,080	)

Future amortization associated with net carrying amount of intangible assets

Future amortization associated with the net carrying amount of intangible assets is estimated to be approximately as follows (in thousands):

Remainder of fiscal year 2012	$	2,601
Fiscal year 2013	4,578
Fiscal year 2014	4,529
Fiscal year 2015	4,405
Fiscal year 2016	4,280
Future fiscal years	43,603
	$	63,996

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Shareholders' Equity (Details) (USD $)	3 Months Ended		4 Months Ended	6 Months Ended		12 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Jan. 15, 2012	Apr. 08, 2012	Apr. 10, 2011	Sep. 25, 2011
Dividends Per Common Share [Abstract]
Dividends declared per common share (in dollars per share)	$ 0.14	$ 0.10		$ 0.28	$ 0.20	$ 0.40
Dividends payable	$ 25,610,000			$ 25,610,000		$ 17,827,000
Dividends, Common Stock, Cash				50,843,000		70,447,000
Dividends Payable, Date of Record, Day, Month and Year	Apr. 05, 2012
Dividends Payable, Date to be Paid, Day, Month and Year	Apr. 17, 2012
Common Stock [Abstract]
Common stock, shares authorized	600,000,000			600,000,000		300,000,000
Treasury Stock [Abstract]
Stock Repurchase Program, Authorized Amount			200,000,000
Treasury Stock, Shares, Acquired			56,500
Treasury Stock Acquired, Average Cost Per Share				$ 63.70
Treasury Stock, Value, Acquired, Cost Method				$ 3,599,000

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Intangible Assets (Details) (USD $)	3 Months Ended		6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011	Sep. 25, 2011
Finite and Indefinite-Lived Intangible Assets
Gross carrying amount	$ 100,356,000		$ 100,356,000		$ 99,314,000
Accumulated amortization	(34,309,000)		(34,309,000)		(32,080,000)
Amortization of intangible assets	1,300,000	2,000,000	3,100,000	3,800,000
Definite-lived contract-based
Finite and Indefinite-Lived Intangible Assets
Gross carrying amount	96,758,000		96,758,000		96,019,000
Accumulated amortization	(33,290,000)		(33,290,000)		(31,660,000)
Definite-lived marketing-related and other
Finite and Indefinite-Lived Intangible Assets
Gross carrying amount	1,547,000		1,547,000		1,547,000
Accumulated amortization	(1,019,000)		(1,019,000)		(420,000)
Indefinite-lived contract-based
Finite and Indefinite-Lived Intangible Assets
Gross carrying amount	$ 2,051,000		$ 2,051,000		$ 1,748,000

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Related Party Transactions (Details)	6 Months Ended
	Apr. 08, 2012 Foundation
Related Party Transactions [Abstract]
Number of non-profit organizations	2

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Recent Accounting Pronouncements

6 Months Ended

Apr. 08, 2012

New Accounting Pronouncements and Changes in Accounting Principles [Abstract]

Recent Accounting Pronoucements

Recent Accounting Pronouncements

In December 2010, the Financial Accounting Standards Board (“FASB”) issued amended guidance within Accounting Standards Codification (“ASC”) 805, “Business Combinations,” which updates previous guidance on this topic and applies to all material transactions. The amendments specify that if a public entity presents comparative financial statements, the entity should disclose revenue and earnings of the combined entity as though the business combination(s) had occurred as of the beginning of the comparable prior annual reporting period only. Additional amendments expand supplemental pro forma disclosures to include a description of the nature and amount of material, nonrecurring pro forma adjustments directly attributable to the business combination included in the reported pro forma revenue and earnings. The updated guidance is effective for fiscal years beginning after December 15, 2010 and is applied prospectively to business combinations completed on or after that date. The provisions are effective for the Company’s fiscal year ending September 30, 2012. We do not expect the adoption of these provisions to have a significant effect on our consolidated financial statements.

In June 2011, the FASB issued Accounting Standards Update (“ASU”) No. 2011-05, “Presentation of Comprehensive Income,” which amends ASC 220, “Comprehensive Income.” The amended guidance requires that all nonowner changes in stockholders’ equity be presented in either a single statement of comprehensive income or two separate but consecutive statements. The objective of these amendments is to improve the comparability, consistency, and transparency of financial reporting and to increase the prominence of items reported in other comprehensive income. In December 2011, the FASB issued ASU No. 2011-12, “Deferral of the Effective Date for Amendments to the Presentation of Reclassifications of Items Out of Accumulated Other Comprehensive Income in Accounting Standards Update No. 2011-05,” which defers the implementation requirement in ASU No. 2011-05 to present on the face of the financial statements the effects of reclassifications out of accumulated other comprehensive income on the components of net income and other comprehensive income. The amended guidance specifies that entities should continue to report reclassifications out of accumulated other comprehensive income consistent with presentation requirements in effect before ASU No. 2011-05. The guidance provided in ASU No. 2011-05 and ASU No. 2011-12 is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. The provisions are effective for the Company’s first quarter of the fiscal year ending September 29, 2013.

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Shareholders' Equity (Details 2) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended		12 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011	Sep. 25, 2011
Comprehensive Income
Net income	$ 117,665	$ 89,935	$ 235,992	$ 178,665	$ 342,612
Foreign currency translation adjustments	2,753	3,139	3,111	5,389	(1,209)
Reclassification adjustments for amounts included in net income				245	245
Change in unrealized gains and losses, net of income taxes	8	239	(15)	(17)	9
Comprehensive income	$ 120,426	$ 93,313	$ 239,088	$ 184,282	$ 341,657

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Share-Based Payments (Tables)

6 Months Ended

Apr. 08, 2012

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Share-based payment expense included in the consolidated statements of operations

Share-based payment expense was included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended						Twenty-eight weeks ended
	April 8, 2012			April 10, 2011			April 8, 2012			April 10, 2011
Cost of goods sold and occupancy costs	$	372		$	288		$	945		$	658
Direct store expenses	4,473			2,894			10,363			6,619
General and administrative expenses	3,697			2,307			8,451			5,571
Share-based payment expense before income taxes	8,542			5,489			19,759			12,848
Income tax benefit	(3,236		)	(1,999		)	(7,454		)	(4,870		)
Net share-based payment expense	$	5,306		$	3,490		$	12,305		$	7,978

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Earnings per Share (Tables)

6 Months Ended

Apr. 08, 2012

Earnings Per Share [Abstract]

Reconciliation of the numerators and denominators of the basic and diluted earnings per share calculations

A reconciliation of the numerators and denominators of the basic and diluted earnings per share calculations follows (in thousands, except per share amounts):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Net income (numerator for basic and diluted earnings per share)	$	117,665	$	89,935	$	235,992	$	178,665
Weighted average common shares outstanding (denominator for basic earnings per share)	182,161		174,686		180,649		173,606
Potential common shares outstanding:
Incremental shares from assumed exercise of stock options	2,442		2,438		2,192		2,008
Weighted average common shares outstanding and potential additional common shares outstanding (denominator for diluted earnings per share)	184,603		177,124		182,841		175,614
Basic earnings per share	$	0.65	$	0.51	$	1.31	$	1.03
Diluted earnings per share	$	0.64	$	0.51	$	1.29	$	1.02

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Earnings per Share (Details) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended		6 Months Ended		12 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011	Sep. 25, 2011
Earnings per share reconciliation
Net Income (numerator for basic and diluted earnings per share)	$ 117,665	$ 89,935	$ 235,992	$ 178,665	$ 342,612
Weighted average common shares outstanding (denominator for basic earnings per share)	182,161,000	174,686,000	180,649,000	173,606,000
Potential common shares outstanding:
Incremental shares from assumed exercise of stock options	2,442,000	2,438,000	2,192,000	2,008,000
Weighted average common shares outstanding and potential additional common shares outstanding (denominator for diluted earnings per share)	184,603,000	177,124,000	182,841,000	175,614,000
Basic earnings per share (in dollars per share)	$ 0.65	$ 0.51	$ 1.31	$ 1.03
Diluted earnings per share (in dollars per share)	$ 0.64	$ 0.51	$ 1.29	$ 1.02
Stock Options
Antidilutive securities excluded from computation of earnings per share
Common stock not included in computation of diluted earnings per share (in shares)		4,900,000		6,800,000

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Basis of Presentation (Details)	6 Months Ended	12 Months Ended
	Apr. 08, 2012 Segment	Sep. 25, 2011
Organization Consolidation and Presentation [Line Items]
Number of operating segments	1
Number of reportable segments	1
Number of weeks in fiscal year	P53W	P52W
Number of weeks in first quarter	P16W
Number of weeks in second quarter	P12W
Number of weeks in third quarter	P12W
Minimum [Member]
Organization Consolidation and Presentation [Line Items]
Number of weeks in fiscal year	P52W
Number of weeks in fourth quarter	P12W
Maximum [Member]
Organization Consolidation and Presentation [Line Items]
Number of weeks in fiscal year	P53W
Number of weeks in fourth quarter	P13W

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Basis of Presentation (Details 2)	3 Months Ended		6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011
Percentage sales by geographic area
Percentage of Total Sales	100.00%	100.00%	100.00%	100.00%
United States
Percentage sales by geographic area
Percentage of Total Sales	96.80%	96.90%	96.80%	96.90%
Canada and United Kingdom
Percentage sales by geographic area
Percentage of Total Sales	3.20%	3.10%	3.20%	3.10%

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Basis of Presentation

6 Months Ended

Apr. 08, 2012

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Presentation

Basis of Presentation

The accompanying unaudited consolidated financial statements of Whole Foods Market, Inc. and its consolidated subsidiaries (collectively “Whole Foods Market,” “Company,” or “We”) have been prepared in accordance with U.S. generally accepted accounting principles (“GAAP”) for interim financial statements and with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. The information included in this Form 10-Q should be read in conjunction with Management’s Discussion and Analysis, the consolidated financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the fiscal year ended September 25, 2011. In the opinion of management, the accompanying consolidated financial statements reflect all adjustments, consisting of normal recurring accruals, considered necessary for a fair presentation. Where appropriate, we have reclassified prior years’ financial statements to conform to current year presentation. Interim results are not necessarily indicative of results for any other interim period or for a full fiscal year. The Company reports its results of operations on a 52- or 53-week fiscal year ending on the last Sunday in September. The first fiscal quarter is 16 weeks, the second and third quarters each are 12 weeks, and the fourth quarter is 12 or 13 weeks. Fiscal year 2012 is a 53-week year and fiscal year 2011 was a 52-week year. The Company has one operating segment and a single reportable segment, natural and organic foods supermarkets. The following is a summary of percentage sales by geographic area for the twelve and twenty-eight weeks ended:

	April 8, 2012		April 10, 2011
Sales:
United States	96.8	%	96.9	%
Canada and United Kingdom	3.2		3.1
Total sales	100.0	%	100.0	%

The following is a summary of the percentage of net long-lived assets by geographic area as of the dates indicated:

	April 8, 2012		September 25, 2011
Long-lived assets, net:
United States	95.7	%	95.9	%
Canada and United Kingdom	4.3		4.1
Total long-lived assets, net	100.0	%	100.0	%

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Basis of Presentation (Details 3)	Apr. 08, 2012	Sep. 25, 2011
Percentage net long-lived assets by geographic area
Percentage of Total Net Long-Lived Assets	100.00%	100.00%
United States
Percentage net long-lived assets by geographic area
Percentage of Total Net Long-Lived Assets	95.70%	95.90%
Canada and United Kingdom
Percentage net long-lived assets by geographic area
Percentage of Total Net Long-Lived Assets	4.30%	4.10%

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Long-Term Debt (Details) (USD $) In Millions, unless otherwise specified	6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Sep. 25, 2011	Sep. 26, 2010
Debt Disclosure [Abstract]
Term loan, face amount				$ 700
Term loan				490
Repayment of term loan		300
Term loan repayment period (in years)	5 years
Revolving line of credit secured by pledge, maximum available	350
Amount available to entity under line of credit facility	350.0		348.6
Outstanding letters of credit			$ 1.4

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Consolidated Balance Sheets (USD $) In Thousands, unless otherwise specified	Apr. 08, 2012	Sep. 25, 2011
Current assets:
Cash and cash equivalents	$ 175,375	$ 212,004
Short-term investments - available-for-sale securities	881,945	442,320
Restricted cash	104,942	91,956
Accounts receivable	189,717	175,310
Merchandise inventories	365,619	336,799
Prepaid expenses and other current assets	59,813	73,579
Deferred income taxes	122,766	121,176
Total current assets	1,900,177	1,453,144
Property and equipment, net of accumulated depreciation and amortization	2,053,507	1,997,212
Long-term investments - available-for-sale securities	139,956	52,815
Goodwill	662,938	662,938
Intangible assets, net of accumulated amortization	66,047	67,234
Deferred income taxes	43,047	50,148
Other assets	8,447	8,584
Total assets	4,874,119	4,292,075
Current liabilities:
Current installments of capital lease obligations	346	466
Accounts payable	243,627	236,913
Accrued payroll, bonus and other benefits due team members	300,501	281,587
Dividends payable	25,610	17,827
Other current liabilities	382,139	342,568
Total current liabilities	952,223	879,361
Long-term capital lease obligations, less current installments	18,882	17,439
Deferred lease liabilities	395,881	353,776
Other long-term liabilities	52,175	50,194
Total liabilities	1,419,161	1,300,770
Shareholders’ equity:
Common stock, no par value, 600,000 shares authorized; 182,980 and 178,886 shares issued; 182,923 and 178,886 shares oustanding at 2012 and 2011, respectively	2,399,979	2,120,972
Common stock in treasury, at cost	(3,599)
Accumulated other comprehensive income (loss)	2,932	(164)
Retained earnings	1,055,646	870,497
Total shareholders' equity	3,454,958	2,991,305
Commitments and contingencies
Total liabilities and shareholders' equity	$ 4,874,119	$ 4,292,075

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Share-Based Payments (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011
Employee Service Share Based Compensation Allocation of Recognized Period Costs
Share-based payment expense before income taxes	$ 8,542	$ 5,489	$ 19,759	$ 12,848
Income tax benefit	(3,236)	(1,999)	(7,454)	(4,870)
Net share-based payment expense	5,306	3,490	12,305	7,978
Cost of goods sold and occupancy costs [Member]
Employee Service Share Based Compensation Allocation of Recognized Period Costs
Share-based payment expense before income taxes	372	288	945	658
Direct store expenses [Member]
Employee Service Share Based Compensation Allocation of Recognized Period Costs
Share-based payment expense before income taxes	4,473	2,894	10,363	6,619
General and administrative expenses [Member]
Employee Service Share Based Compensation Allocation of Recognized Period Costs
Share-based payment expense before income taxes	$ 3,697	$ 2,307	$ 8,451	$ 5,571

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Consolidated Statements of Shareholders' Equity and Comprehensive Income (Parenthetical) (USD $)	3 Months Ended		6 Months Ended		12 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011	Sep. 25, 2011
Statement of Stockholders' Equity [Abstract]
Dividends declared per common share (in dollars per share)	$ 0.14	$ 0.10	$ 0.28	$ 0.20	$ 0.40

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Investments (Details) (USD $) In Millions, unless otherwise specified	6 Months Ended	12 Months Ended
	Apr. 08, 2012 Month	Sep. 25, 2011 Month
Investments [Abstract]
Aggregate available-for-sale securities with unrealized holding losses	$ 163.7	$ 74.5
Short-term Investment Average Effective Maturity Period (in months)	2	4
Long-term Investment Average Effective Maturity Period (in months)	16	15

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Basis of Presentation (Tables)

6 Months Ended

Apr. 08, 2012

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Summary of percentage sales by geographic area

The following is a summary of percentage sales by geographic area for the twelve and twenty-eight weeks ended:

	April 8, 2012		April 10, 2011
Sales:
United States	96.8	%	96.9	%
Canada and United Kingdom	3.2		3.1
Total sales	100.0	%	100.0	%

Summary of percentage of net long-lived assets by geographic area

The following is a summary of the percentage of net long-lived assets by geographic area as of the dates indicated:

	April 8, 2012		September 25, 2011
Long-lived assets, net:
United States	95.7	%	95.9	%
Canada and United Kingdom	4.3		4.1
Total long-lived assets, net	100.0	%	100.0	%

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Investments (Details 2) (USD $) In Thousands, unless otherwise specified	Apr. 08, 2012	Sep. 25, 2011
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Current	$ 881,945	$ 442,320
Available-for-sale Securities, Noncurrent	139,956	52,815
Available-for-sale Securities, Current [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Amortized Cost Basis	881,824	442,043
Available-for-sale Securities, Gross Unrealized Gains	175	293
Available-for-sale Securities, Gross Unrealized Losses	(54)	(16)
Available-for-sale Securities, Current	881,945	442,320
Available-for-sale Securities, Current [Member] | Municipal Notes [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Amortized Cost Basis	323,559	268,945
Available-for-sale Securities, Gross Unrealized Gains	165	279
Available-for-sale Securities, Gross Unrealized Losses	(54)	(16)
Available-for-sale Securities, Current	323,670	269,208
Available-for-sale Securities, Current [Member] | Commercial Paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Amortized Cost Basis	22,975	67,950
Available-for-sale Securities, Gross Unrealized Gains	10	14
Available-for-sale Securities, Gross Unrealized Losses
Available-for-sale Securities, Current	22,985	67,964
Available-for-sale Securities, Current [Member] | Variable Rate Demand Obligation [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Amortized Cost Basis	535,290	105,148
Available-for-sale Securities, Gross Unrealized Gains
Available-for-sale Securities, Gross Unrealized Losses
Available-for-sale Securities, Current	535,290	105,148
Available-for-sale Securities, Noncurrent [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Amortized Cost Basis	139,776	52,732
Available-for-sale Securities, Gross Unrealized Gains	206	93
Available-for-sale Securities, Gross Unrealized Losses	(26)	(10)
Available-for-sale Securities, Noncurrent	139,956	52,815
Available-for-sale Securities, Noncurrent [Member] | Municipal Bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Amortized Cost Basis	134,506	47,387
Available-for-sale Securities, Gross Unrealized Gains	167	77
Available-for-sale Securities, Gross Unrealized Losses	(26)	(10)
Available-for-sale Securities, Noncurrent	134,647	47,454
Available-for-sale Securities, Noncurrent [Member] | Corporate Bond Securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale Securities, Amortized Cost Basis	5,270	5,345
Available-for-sale Securities, Gross Unrealized Gains	39	16
Available-for-sale Securities, Gross Unrealized Losses
Available-for-sale Securities, Noncurrent	$ 5,309	$ 5,361

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Investments (Tables)

6 Months Ended

Apr. 08, 2012

Investments [Abstract]

Schedule of available-for-sale securities reconciliation

The Company held the following investments as of the dates indicated (in thousands):

April 8, 2012	Adjusted cost		Unrealized gains		Unrealized losses			Fair value
Short-term marketable securities - available-for-sale:
Municipal bonds	$	323,559	$	165	$	(54	)	$	323,670
Commercial paper	22,975		10		—			22,985
Variable rate demand notes	535,290		—		—			535,290
Total short-term marketable securities	$	881,824	$	175	$	(54	)	$	881,945
Long-term marketable securities - available-for-sale:
Municipal bonds	$	134,506	$	167	$	(26	)	$	134,647
Corporate bonds	5,270		39		—			5,309
Total long-term marketable securities	$	139,776	$	206	$	(26	)	$	139,956

September 25, 2011	Adjusted cost		Unrealized gains		Unrealized losses			Fair value
Short-term marketable securities - available-for-sale:
Municipal bonds	$	268,945	$	279	$	(16	)	$	269,208
Commercial paper	67,950		14		—			67,964
Variable rate demand notes	105,148		—		—			105,148
Total short-term marketable securities	$	442,043	$	293	$	(16	)	$	442,320
Long-term marketable securities - available-for-sale:
Municipal bonds	$	47,387	$	77	$	(10	)	$	47,454
Corporate bonds	5,345		16		—			5,361
Total long-term marketable securities	$	52,732	$	93	$	(10	)	$	52,815

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Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011
Cash flows from operating activities
Net income	$ 235,992	$ 178,665
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization	162,509	152,903
Loss on disposition of fixed assets	1,103	914
Share-based payment expense	19,759	12,848
LIFO expense	1,000	3,000
Deferred income tax expense	5,624	15,747
Excess tax benefit related to exercise of team member stock options	(15,481)	(9,251)
Deferred lease liabilities	37,429	24,110
Other	4,780	202
Net change in current assets and liabilities:
Accounts receivable	(18,816)	(24,991)
Merchandise inventories	(29,489)	(20,474)
Prepaid expenses and other current assets	14,278	(7,310)
Accounts payable	6,334	20,176
Accrued payroll, bonus and other benefits due team members	18,718	9,580
Other current liabilities	71,101	46,457
Net change in other long-term liabilities	1,840	241
Net cash provided by operating activities	516,681	402,817
Cash flows from investing activities
Development costs of new locations	(114,549)	(89,451)
Other property and equipment expenditures	(98,729)	(80,130)
Purchase of available-for-sale securities	(1,321,589)	(780,154)
Sale of available-for-sale securities	789,432	731,306
Decrease (increase) in restricted cash	(12,986)	17
Other investing activities	(1,614)	(1,576)
Net cash used in investing activities	(760,035)	(219,988)
Cash flows from financing activities
Common stock dividends paid	(43,057)	(17,348)
Issuance of common stock	237,004	153,067
Purchase of treasury stock	(3,599)
Excess tax benefit related to exercise of team member stock options	15,481	9,251
Payments on long-term debt and capital lease obligations	(113)	(300,123)
Net cash provided by (used in) financing activities	205,716	(155,153)
Effect of exchange rate changes on cash and cash equivalents	1,009	2,431
Net change in cash and cash equivalents	(36,629)	30,107
Cash and cash equivalents at beginning of period	212,004	131,996
Cash and cash equivalents at end of period	175,375	162,103
Supplemental disclosures of cash flow information:
Interest paid	1,616	14,002
Federal and state income taxes paid	$ 91,172	$ 109,611

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Consolidated Balance Sheets (Parenthetical) (USD $) In Thousands, unless otherwise specified	Apr. 08, 2012	Sep. 25, 2011
Statement of Financial Position [Abstract]
Common stock, shares authorized	600,000	300,000
Common stock, shares issued	182,980	178,886
Common stock, shares outstanding	182,923	178,886
Common stock, no par value

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Earnings per Share

6 Months Ended

Apr. 08, 2012

Earnings Per Share [Abstract]

Earnings Per Share

Earnings per Share

The computation of basic earnings per share is based on the number of weighted average common shares outstanding during the period. The computation of diluted earnings per share includes the dilutive effect of common stock equivalents consisting of incremental common shares deemed outstanding from the assumed exercise of stock options.

A reconciliation of the numerators and denominators of the basic and diluted earnings per share calculations follows (in thousands, except per share amounts):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Net income (numerator for basic and diluted earnings per share)	$	117,665	$	89,935	$	235,992	$	178,665
Weighted average common shares outstanding (denominator for basic earnings per share)	182,161		174,686		180,649		173,606
Potential common shares outstanding:
Incremental shares from assumed exercise of stock options	2,442		2,438		2,192		2,008
Weighted average common shares outstanding and potential additional common shares outstanding (denominator for diluted earnings per share)	184,603		177,124		182,841		175,614
Basic earnings per share	$	0.65	$	0.51	$	1.31	$	1.03
Diluted earnings per share	$	0.64	$	0.51	$	1.29	$	1.02

For the twelve and twenty-eight weeks ended April 8, 2012 the number of stock options excluded from the computation of diluted earnings per share due to their antidilutive effect was not material. The computation of diluted earnings per share for the twelve and twenty-eight weeks ended April 10, 2011 does not include options to purchase approximately 4.9 million shares and 6.8 million shares of common stock due to their antidilutive effect.

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Document and Entity Information	6 Months Ended
	Apr. 08, 2012	May 11, 2012
Document And Entity Information [Abstract]
Entity Registrant Name	WHOLE FOODS MARKET INC
Entity Central Index Key	0000865436
Document Type	10-Q
Entity Filer Category	Large Accelerated Filer
Current Fiscal Year End Date	--09-30
Document Period End Date	Apr. 08, 2012
Document Fiscal Year Focus	2012
Entity Common Stock, Shares Outstanding		183,563,879
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Current Reporting Status	Yes

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Share-Based Payments

6 Months Ended

Apr. 08, 2012

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Share-Based Payments

Share-Based Payments

Total share-based payment expense before income taxes recognized during the twelve and twenty-eight weeks ended April 8, 2012 was approximately $8.5 million and $19.8 million, respectively. Share-based payment expense before income taxes recognized during the twelve and twenty-eight weeks ended April 10, 2011 was approximately $5.5 million and $12.8 million, respectively. Share-based payment expense was included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended						Twenty-eight weeks ended
	April 8, 2012			April 10, 2011			April 8, 2012			April 10, 2011
Cost of goods sold and occupancy costs	$	372		$	288		$	945		$	658
Direct store expenses	4,473			2,894			10,363			6,619
General and administrative expenses	3,697			2,307			8,451			5,571
Share-based payment expense before income taxes	8,542			5,489			19,759			12,848
Income tax benefit	(3,236		)	(1,999		)	(7,454		)	(4,870		)
Net share-based payment expense	$	5,306		$	3,490		$	12,305		$	7,978

At April 8, 2012 and September 25, 2011, approximately 11.8 million shares and 11.7 million shares of the Company’s common stock, respectively, were available for future stock incentive grants. At April 8, 2012 and September 25, 2011, there was approximately $75.1 million and $97.4 million of unrecognized share-based payment expense, respectively, related to nonvested stock options, net of estimated forfeitures, related to approximately 6.4 million shares and 6.5 million shares, respectively. We anticipate this expense to be recognized over a weighted average period of approximately three years.

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Consolidated Statements of Operations (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011
Income Statement [Abstract]
Sales	$ 2,670,282	$ 2,350,518	$ 6,061,222	$ 5,354,173
Cost of goods sold and occupancy costs	1,700,574	1,513,446	3,913,397	3,478,616
Gross profit	969,708	837,072	2,147,825	1,875,557
Direct store expenses	681,771	608,737	1,552,696	1,399,366
General and administrative expenses	86,760	75,661	190,276	164,172
Pre-opening expenses	10,496	9,543	20,901	18,183
Relocation, store closure and lease termination costs	1,298	1,003	4,231	4,149
Operating income	189,383	142,128	379,721	289,687
Investment and other income, net of interest	2,254	658	4,633	977
Income before income taxes	191,637	142,786	384,354	290,664
Provision for income taxes	73,972	52,851	148,362	111,999
Net income	$ 117,665	$ 89,935	$ 235,992	$ 178,665
Basic earnings per share (in dollars per share)	$ 0.65	$ 0.51	$ 1.31	$ 1.03
Weighted average shares outstanding (in shares)	182,161	174,686	180,649	173,606
Diluted earnings per share (in dollars per share)	$ 0.64	$ 0.51	$ 1.29	$ 1.02
Weighted average shares outstanding, diluted basis (in shares)	184,603	177,124	182,841	175,614
Dividends declared per common share (in dollars per share)	$ 0.14	$ 0.10	$ 0.28	$ 0.20

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Intangible Assets

6 Months Ended

Apr. 08, 2012

Intangible Assets, Net (Excluding Goodwill) [Abstract]

Intangible Assets

Intangible Assets

The components of intangible assets were as follows (in thousands):

	April 8, 2012					September 25, 2011
	Gross carrying amount		Accumulated amortization			Gross carrying amount		Accumulated amortization
Definite-lived contract-based	$	96,758	$	(33,290	)	$	96,019	$	(31,660	)
Definite-lived marketing-related and other	1,547		(1,019		)	1,547		(420		)
Indefinite-lived contract-based	2,051					1,748
	$	100,356	$	(34,309	)	$	99,314	$	(32,080	)

Amortization associated with intangible assets totaled approximately $1.3 million and $3.1 million for the twelve and twenty-eight weeks ended April 8, 2012, respectively, and approximately $2.0 million and $3.8 million, respectively, for the same periods of the prior fiscal year. Future amortization associated with the net carrying amount of intangible assets is estimated to be approximately as follows (in thousands):

Remainder of fiscal year 2012	$	2,601
Fiscal year 2013	4,578
Fiscal year 2014	4,529
Fiscal year 2015	4,405
Fiscal year 2016	4,280
Future fiscal years	43,603
	$	63,996

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Investments (Notes)

6 Months Ended

Apr. 08, 2012

Investments [Abstract]

Investments

Investments

The Company holds investments in marketable securities, generally municipal bonds, corporate bonds, commercial paper and variable rate demand notes, that are classified as either short- or long-term available-for-sale securities. The Company held the following investments as of the dates indicated (in thousands):

April 8, 2012	Adjusted cost		Unrealized gains		Unrealized losses			Fair value
Short-term marketable securities - available-for-sale:
Municipal bonds	$	323,559	$	165	$	(54	)	$	323,670
Commercial paper	22,975		10		—			22,985
Variable rate demand notes	535,290		—		—			535,290
Total short-term marketable securities	$	881,824	$	175	$	(54	)	$	881,945
Long-term marketable securities - available-for-sale:
Municipal bonds	$	134,506	$	167	$	(26	)	$	134,647
Corporate bonds	5,270		39		—			5,309
Total long-term marketable securities	$	139,776	$	206	$	(26	)	$	139,956

September 25, 2011	Adjusted cost		Unrealized gains		Unrealized losses			Fair value
Short-term marketable securities - available-for-sale:
Municipal bonds	$	268,945	$	279	$	(16	)	$	269,208
Commercial paper	67,950		14		—			67,964
Variable rate demand notes	105,148		—		—			105,148
Total short-term marketable securities	$	442,043	$	293	$	(16	)	$	442,320
Long-term marketable securities - available-for-sale:
Municipal bonds	$	47,387	$	77	$	(10	)	$	47,454
Corporate bonds	5,345		16		—			5,361
Total long-term marketable securities	$	52,732	$	93	$	(10	)	$	52,815

At April 8, 2012 and September 25, 2011 available-for-sale securities totaling approximately $163.7 million and $74.5 million, respectively, were in unrealized loss positions.

At April 8, 2012, the average effective maturity of the Company’s short- and long-term investments was approximately 2 months and 16 months, respectively, compared to approximately 4 months and 15 months, respectively at September 25, 2011.

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Fair Value Measurements (Tables)

6 Months Ended

Apr. 08, 2012

Fair Value Disclosures [Abstract]

Financial assets measured at fair value on a recurring basis

The Company held the following financial assets at fair value, based on the hierarchy input levels indicated, on a recurring basis (in thousands):

April 8, 2012	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Cash equivalents:
Money market fund	$	20,078	$	—	$	—	$	20,078
Municipal bonds	—		8,411		—		8,411
Restricted cash:
Money market fund	104,942		—		—		104,942
Marketable securities - available-for-sale:
Municipal bonds	—		458,317		—		458,317
Corporate bonds	—		5,309		—		5,309
Commercial paper	—		22,985		—		22,985
Variable rate demand notes	—		535,290		—		535,290
Total	$	125,020	$	1,030,312	$	—	$	1,155,332

September 25, 2011	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Cash equivalents:
Money market fund	$	59,157	$	—	$	—	$	59,157
Municipal bonds	—		3,791		—		3,791
Commercial paper	—		12,998		—		12,998
Restricted cash:
Money market fund	91,956		—		—		91,956
Marketable securities - available-for-sale:
Municipal bonds	—		316,662		—		316,662
Corporate bonds	—		5,361		—		5,361
Commercial paper	—		67,964		—		67,964
Variable rate demand notes	—		105,148		—		105,148
Total	$	151,113	$	511,924	$	—	$	663,037

Fair value, assets and liabilities measured on nonrecurring basis

Fair value adjustments, based on hierarchy input Level 3, reduced the carrying value of related property and equipment to zero and were included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Direct store expenses	$	1	$	9	$	20	$	501
General and administrative expenses	1,178		—		1,178		—
Relocation, store closure and lease term costs	—		13		—		80
Total impairment of long-lived assets	$	1,179	$	22	$	1,198	$	581

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Commitments and Contingencies

6 Months Ended

Apr. 08, 2012

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Commitments and Contingencies

The Company is exposed to claims and litigation matters arising in the ordinary course of business and uses various methods to resolve these matters in a manner that we believe best serves the interests of our stakeholders. Our primary contingencies are associated with insurance and self-insurance obligations and litigation matters. Estimation of our insurance and self-insurance liabilities requires significant judgments, and actual claim settlements and associated expenses may differ from our current provisions for loss. We have exposures to loss contingencies arising from pending or threatened litigation for which assessing and estimating the outcomes of these matters involve substantial uncertainties.

On October 27, 2008, Whole Foods Market was served with the complaint in Kottaras v. Whole Foods Market, Inc., a putative class action filed in the United States District Court for the District of Columbia, seeking treble damages, equitable, injunctive, and declaratory relief and alleging that the acquisition and merger between Whole Foods Market and Wild Oats violates various provisions of the federal antitrust laws. During the first quarter of fiscal year 2012, the federal district judge denied the plaintiff’s motion for class certification. Currently that decision is being appealed. The Company has not accrued any loss related to the outcome of this case as of April 8, 2012.

The Company evaluates contingencies on an ongoing basis and has established loss provisions for matters in which losses are probable and the amount of loss can be reasonably estimated. Insurance and legal settlement liabilities are included in the “Other current liabilities” line item on the Consolidated Balance Sheets. We believe the recorded reserves in our consolidated financial statements are adequate in light of the probable and estimable liabilities.

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Income Taxes

6 Months Ended

Apr. 08, 2012

Income Tax Disclosure [Abstract]

Income Taxes

Income Taxes

Income taxes for both the twelve and twenty-eight weeks ended April 8, 2012 resulted in an effective tax rate of approximately 38.6%, compared to approximately 37.0% and 38.5%, respectively, for the same periods of the prior fiscal year. At April 8, 2012, income taxes payable totaled approximately $10.3 million compared to an income tax receivable of approximately $14.8 million at September 25, 2011.

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Reserves for Closed Properties

6 Months Ended

Apr. 08, 2012

Restructuring and Related Activities [Abstract]

Reserves for Closed Properties

Reserves for Closed Properties

Following is a summary of store closure reserve activity during the twenty-eight weeks ended April 8, 2012 and fiscal year ended September 25, 2011 (in thousands):

	April 8, 2012			September 25, 2011
Beginning balance	$	44,702		$	59,298
Additions	1,964			4,706
Usage	(5,154		)	(17,805		)
Adjustments	1,203			(1,497		)
Ending balance	$	42,715		$	44,702

Additions to store closure reserves relate to the accretion of interest on existing reserves and new closures. Usage included approximately $5.2 million in ongoing cash rental payments during the twenty-eight weeks ended April 8, 2012. During the fiscal year ended September 25, 2011, usage included approximately $10.1 million in ongoing cash rental payments and approximately $7.7 million in termination fees related to certain idle properties. Additionally, the Company recorded reserve adjustments of approximately $3.7 million during the fiscal year ended September 25, 2011, offset to goodwill.

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Long-Term Debt

6 Months Ended

Apr. 08, 2012

Debt Disclosure [Abstract]

Long-Term Debt

Long-Term Debt

The Company has a $350 million revolving line of credit that extends to August 28, 2012. The Company’s obligations under the facility are secured by liens on certain of the Company’s assets, including stock of its subsidiaries. The credit agreement contains certain affirmative covenants including maintenance of certain financial ratios and certain negative covenants including limitations on additional indebtedness and payments as defined by the agreement. At April 8, 2012 the Company was in compliance with all applicable debt covenants. At April 8, 2012 and September 25, 2011 the Company had no amounts drawn under this agreement. The amount available to the Company under the agreement was $350 million at April 8, 2012. The amount available to the Company at September 25, 2011 was effectively reduced to approximately $348.6 million by outstanding letters of credit totaling approximately $1.4 million. The Company had outstanding a $700 million, five-year term loan agreement due in 2012, with an outstanding balance of $490 million at September 26, 2010. During the twenty-eight weeks ended April 10, 2011, the Company repaid $300 million on the term loan and repaid the remainder throughout fiscal year 2011.

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Shareholders' Equity

6 Months Ended

Apr. 08, 2012

Equity [Abstract]

Shareholders' Equity

Shareholders’ Equity

Dividends per Common Share

During the twelve weeks ended April 8, 2012, the Company’s Board of Directors declared a cash dividend to shareholders of $0.14 per common share, payable on April 17, 2012 to shareholders of record on April 5, 2012. Approximately $25.6 million was included in the “Dividends payable” line item on the Consolidated Balance Sheets at April 8, 2012. During fiscal year 2011, the Company’s Board of Directors declared cash dividends to shareholders totaling $0.40 per common share resulting in dividend payments of approximately $70.4 million, of which approximately $17.8 million was included in the “Dividends payable” line item on the Consolidated Balance Sheets at September 25, 2011.

Common Stock

During the twelve weeks ended April 8, 2012, the Company approved an increase in the number of authorized shares of the Company’s common stock from 300 million to 600 million.

Treasury Stock

During the first quarter of fiscal year 2012, the Company’s Board of Directors authorized a $200 million stock repurchase program through November 1, 2013. The Company repurchased 56,500 shares of Company common stock on the open market during the first quarter of fiscal year 2012. The average price per share paid for shares held in treasury at April 8, 2012 was $63.70, for a total of approximately $3.6 million. The specific timing and repurchase of future amounts will vary based on market conditions, securities law limitations and other factors and will be made using the Company’s available resources. The repurchase program may be suspended or discontinued at any time at the Company’s discretion.

Comprehensive Income

The Company’s comprehensive income was comprised of: net income; unrealized gains and losses on investments; unrealized gains and losses on cash flow hedge instruments, including reclassification adjustments of unrealized losses to net income related to ongoing interest payments; and foreign currency translation adjustments, net of income taxes. Comprehensive income was as follows (in thousands):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012			April 10, 2011
Net income	$	117,665	$	89,935	$	235,992		$	178,665
Foreign currency translation adjustments	2,753		3,139		3,111			5,389
Reclassification adjustments for amounts included in net income	—		—		—			245
Change in unrealized gains and losses, net of income taxes	8		239		(15		)	(17		)
Comprehensive income	$	120,426	$	93,313	$	239,088		$	184,282

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Fair Value Measurements 2 (Details) (Fair Value, Measurements, Nonrecurring [Member], USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011
Asset Impairment Charges [Abstract]
Asset Impairment Charges	$ 1,179	$ 22	$ 1,198	$ 581
Direct store expenses [Member]
Asset Impairment Charges [Abstract]
Asset Impairment Charges	1	9	20	501
General and administrative expenses [Member]
Asset Impairment Charges [Abstract]
Asset Impairment Charges	1,178		1,178
Relocation, store closure and lease term costs [Member]
Asset Impairment Charges [Abstract]
Asset Impairment Charges		$ 13		$ 80

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Summary of Significant Accounting Policies (Policies)

6 Months Ended

Apr. 08, 2012

Accounting Policies [Abstract]

Definition of Fiscal Year

The Company reports its results of operations on a 52- or 53-week fiscal year ending on the last Sunday in September. The first fiscal quarter is 16 weeks, the second and third quarters each are 12 weeks, and the fourth quarter is 12 or 13 weeks. Fiscal year 2012 is a 53-week year and fiscal year 2011 was a 52-week year.

Earnings per Share

The computation of basic earnings per share is based on the number of weighted average common shares outstanding during the period. The computation of diluted earnings per share includes the dilutive effect of common stock equivalents consisting of incremental common shares deemed outstanding from the assumed exercise of stock options.

Fair Value of Financial Instruments

The Company holds money market fund investments that are classified as cash equivalents or restricted cash that are measured at fair value on a recurring basis based on quoted prices in active markets for identical assets. The Company also holds available-for-sale securities generally consisting of state and local municipal obligations and variable rate demand notes which hold high credit ratings. These instruments are valued using a series of multi-dimensional relational models and series of matrices with standard inputs obtained from readily available pricing sources and other observable market data, such as benchmark yields and base spread. Investments are stated at fair value with unrealized gains and losses, net of related tax effect, included as a component of shareholders’ equity until realized. Declines in fair value below the Company’s carrying value deemed to be other-than-temporary are charged against net earnings.

The carrying amounts of trade and other accounts receivable, trade accounts payable, accrued payroll, bonuses and team member benefits, and other accrued expenses approximate fair value because of the short maturity of those instruments. Store closure reserves and estimated workers’ compensation claims are recorded at net present value to approximate fair value.

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Reserves for Closed Properties (Tables)

6 Months Ended

Apr. 08, 2012

Restructuring and Related Activities [Abstract]

Summary of store closure reserve activity

Following is a summary of store closure reserve activity during the twenty-eight weeks ended April 8, 2012 and fiscal year ended September 25, 2011 (in thousands):

	April 8, 2012			September 25, 2011
Beginning balance	$	44,702		$	59,298
Additions	1,964			4,706
Usage	(5,154		)	(17,805		)
Adjustments	1,203			(1,497		)
Ending balance	$	42,715		$	44,702

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Income Taxes (Details) (USD $) In Millions, unless otherwise specified	3 Months Ended		6 Months Ended
	Apr. 08, 2012	Apr. 10, 2011	Apr. 08, 2012	Apr. 10, 2011	Sep. 25, 2011
Income Tax Disclosure [Abstract]
Effective tax rate (as a percent)	38.60%	37.00%	38.60%	38.50%
Accrued Income Taxes, Current	$ 10.3		$ 10.3
Income Taxes Receivable					$ 14.8

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Consolidated Statements of Shareholders' Equity and Comprehensive Income (USD $) In Thousands, except Share data, unless otherwise specified	Total	Common stock	Common stock in treasury	Accumulated other comprehensive income (loss)	Retained earnings
Balances at Sep. 26, 2010	$ 2,373,258	$ 1,773,897		$ 791	$ 598,570
Balances (in shares) at Sep. 26, 2010		172,033,000
Increase (Decrease) in Shareholders' Equity
Net income	342,612				342,612
Foreign currency translation adjustments	(1,209)			(1,209)
Reclassification adjustments for amounts included in net income	245			245
Change in unrealized gains and losses, net of income taxes	9			9
Comprehensive income	341,657
Dividends ($0.28 and $0.40 per common share for the period ended twenty-eight weeks April 08, 2012 and year ended September 25, 2011, respectively)	(70,447)				(70,447)
Issuance of common stock pursuant to team member stock plans	301,591	301,591
Issuance of common stock pursuant to team member stock plans (in shares)		6,857,000
Excess tax benefit related to exercise of team member stock options	18,225	18,225
Share-based payment expense	27,259	27,259
Other	(238)				(238)
Other (in shares)		(4,000)
Balances at Sep. 25, 2011	2,991,305	2,120,972		(164)	870,497
Balances (in shares) at Sep. 25, 2011	178,886,000	178,886,000
Increase (Decrease) in Shareholders' Equity
Net income	235,992				235,992
Foreign currency translation adjustments	3,111			3,111
Reclassification adjustments for amounts included in net income
Change in unrealized gains and losses, net of income taxes	(15)			(15)
Comprehensive income	239,088
Dividends ($0.28 and $0.40 per common share for the period ended twenty-eight weeks April 08, 2012 and year ended September 25, 2011, respectively)	(50,843)				(50,843)
Issuance of common stock pursuant to team member stock plans	232,860	232,860
Issuance of common stock pursuant to team member stock plans (in shares)		4,094,000
Purchase of treasury stock	(3,599)		(3,599)
Purchase of treasury stock (in shares)		(57,000)
Excess tax benefit related to exercise of team member stock options	26,388	26,388
Share-based payment expense	19,759	19,759
Balances at Apr. 08, 2012	$ 3,454,958	$ 2,399,979	$ (3,599)	$ 2,932	$ 1,055,646
Balances (in shares) at Apr. 08, 2012	182,923,000	182,923,000

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Fair Value Measurements

6 Months Ended

Apr. 08, 2012

Fair Value Disclosures [Abstract]

Fair Value Measurements

Fair Value Measurements

Effective January 16, 2012, the Company adopted ASU No. 2011-04, “Amendments to Achieve Common Fair Value Measurement and Disclosure Requirements in U.S. GAAP and IFRSs,” which amends ASC 820, “Fair Value Measurement.” The adoption of ASU No. 2011-04, which primarily consists of clarification and wording changes to existing fair value measurement and disclosure requirements, did not have an impact on the Company’s consolidated financial statements.

Assets and Liabilities Measured at Fair Value on a Recurring Basis

The Company holds money market fund investments that are classified as cash equivalents or restricted cash that are measured at fair value on a recurring basis based on quoted prices in active markets for identical assets. The Company also holds available-for-sale securities generally consisting of state and local municipal obligations and variable rate demand notes which hold high credit ratings. These instruments are valued using a series of multi-dimensional relational models and series of matrices with standard inputs obtained from readily available pricing sources and other observable market data, such as benchmark yields and base spread. Investments are stated at fair value with unrealized gains and losses, net of related tax effect, included as a component of shareholders’ equity until realized. Declines in fair value below the Company’s carrying value deemed to be other-than-temporary are charged against net earnings.

The carrying amounts of trade and other accounts receivable, trade accounts payable, accrued payroll, bonuses and team member benefits, and other accrued expenses approximate fair value because of the short maturity of those instruments. Store closure reserves and estimated workers’ compensation claims are recorded at net present value to approximate fair value.

The Company held the following financial assets at fair value, based on the hierarchy input levels indicated, on a recurring basis (in thousands):

April 8, 2012	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Cash equivalents:
Money market fund	$	20,078	$	—	$	—	$	20,078
Municipal bonds	—		8,411		—		8,411
Restricted cash:
Money market fund	104,942		—		—		104,942
Marketable securities - available-for-sale:
Municipal bonds	—		458,317		—		458,317
Corporate bonds	—		5,309		—		5,309
Commercial paper	—		22,985		—		22,985
Variable rate demand notes	—		535,290		—		535,290
Total	$	125,020	$	1,030,312	$	—	$	1,155,332

September 25, 2011	Level 1 Inputs		Level 2 Inputs		Level 3 Inputs		Total
Cash equivalents:
Money market fund	$	59,157	$	—	$	—	$	59,157
Municipal bonds	—		3,791		—		3,791
Commercial paper	—		12,998		—		12,998
Restricted cash:
Money market fund	91,956		—		—		91,956
Marketable securities - available-for-sale:
Municipal bonds	—		316,662		—		316,662
Corporate bonds	—		5,361		—		5,361
Commercial paper	—		67,964		—		67,964
Variable rate demand notes	—		105,148		—		105,148
Total	$	151,113	$	511,924	$	—	$	663,037

Assets Measured at Fair Value on a Nonrecurring Basis

The Company evaluates long-lived assets for impairment whenever events or changes in circumstances, such as unplanned negative cash flow or short lease life, indicate that the carrying amount of an asset may not be recoverable. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset to fair value. The fair value is determined using management’s best estimate based on a discounted cash flow model based on future store operating results using internal projections. Fair value adjustments, based on hierarchy input Level 3, reduced the carrying value of related property and equipment to zero and were included in the following line items on the Consolidated Statements of Operations for the periods indicated (in thousands):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012		April 10, 2011
Direct store expenses	$	1	$	9	$	20	$	501
General and administrative expenses	1,178		—		1,178		—
Relocation, store closure and lease term costs	—		13		—		80
Total impairment of long-lived assets	$	1,179	$	22	$	1,198	$	581

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Shareholders' Equity (Tables)

6 Months Ended

Apr. 08, 2012

Equity [Abstract]

Components of comprehensive income

Comprehensive income was as follows (in thousands):

	Twelve weeks ended				Twenty-eight weeks ended
	April 8, 2012		April 10, 2011		April 8, 2012			April 10, 2011
Net income	$	117,665	$	89,935	$	235,992		$	178,665
Foreign currency translation adjustments	2,753		3,139		3,111			5,389
Reclassification adjustments for amounts included in net income	—		—		—			245
Change in unrealized gains and losses, net of income taxes	8		239		(15		)	(17		)
Comprehensive income	$	120,426	$	93,313	$	239,088		$	184,282

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Intangible Assets (Details 2) (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Apr. 08, 2012
Future Amortization Expense [Line Items]
Amortization associated with the net carrying amount of intangible assets, remainder of fiscal year	$ 2,601
Amortization associated with the net carrying amount of intangible assets, year two	4,578
Amortization associated with the net carrying amount of intangible assets, year three	4,529
Amortization associated with the net carrying amount of intangible assets, year four	4,405
Amortization associated with the net carrying amount of intangible assets, year five	4,280
Amortization associated with the net carrying amount of intangible assets, after year five	43,603
Amortization associated with the net carrying amount of intangible assets, total	$ 63,996

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Related Party Transactions

6 Months Ended

Apr. 08, 2012

Related Party Transactions [Abstract]

Related Party Transactions

Related Party Transactions

The Company provides ongoing support to two independent non-profit organizations: Whole Planet Foundation and Whole Kids Foundation (the “Foundations”). Whole Planet Foundation’s mission is to empower the poor through microcredit, with a focus on developing-world communities that supply the Company’s stores with product. Whole Kids Foundation is a non-profit organization dedicated to improving children’s nutrition through partnerships with schools, educators, and other organizations. Members of the Company’s management comprise the Board of Directors of each of the Foundations. Additionally, the Company provides administrative support and covers all operating costs and the overhead budget of the Foundations.