Exhibit 99.01

Cepheid 904 Caribbean Drive Sunnyvale, CA 94089 Telephone: 408.541.4191 Fax: 408.541.4192	For Media & Investor Inquiries: Jacquie Ross, CFA Tel: (408) 400 8329 corporate.communications@cepheid.com

CEPHEID REPORTS SECOND QUARTER 2016 RESULTS

SUNNYVALE, California, July 28, 2016 – Cepheid (Nasdaq: CPHD) today reported revenue for the second quarter of 2016 of $146.0 million, representing growth of 10%, or 12% on a constant currency basis, from $132.5 million for the second quarter of 2015. Net loss was $(10.2) million, or $(0.14) per share, which compares to net loss of $(16.7) million, or $(0.23) per share, in the second quarter of 2015.

Excluding stock-based compensation expense, amortization of debt discount and transaction costs, and amortization of purchased intangible assets, non-GAAP net income for the second quarter of 2016 was $3.5 million, or $0.05 per share. This compares to non-GAAP net loss of $(4.5) million, or $(0.06) per share, in the second quarter of 2015, which excluded stock-based compensation expense, amortization of debt discount and transaction costs, and amortization of purchased intangible assets.

“Solid second quarter performance was driven by building momentum across our commercial organization that sets us up well for strong growth in the second half of 2016,” said John Bishop, Cepheid’s Chairman and Chief Executive Officer. “We also continued to move our virology and oncology products closer to market in the United States and Internationally, respectively, and made excellent progress on our next-generation platforms, the Honeycomb and Omni Systems. Taken together, we continue to build an attractive portfolio of products that builds on our leadership in innovation and leverages our substantial worldwide installed base.”

Operational Overview

Total revenue was, in millions:

	Three Months Ended June 30,
	2016		2015		Change (Reported)			Change (Constant Currency)
Systems and Other	$	24.8	$	24.4		2	%		4	%
Reagents and Disposables		121.2		108.1		12	%		14	%
Total Revenue		146.0		132.5		10	%		12	%

By geography, total revenue was, in millions:

	Three Months Ended June 30,
	2016		2015		Change (Reported)			Change (Constant Currency)
North America	$	81.2	$	76.2		7	%		—
International		64.8		56.3		15	%		21	%
Total Revenue		146.0		132.5		10	%		12	%

• GAAP gross margin was 50% and non-GAAP gross margin was 51% for the second quarter of 2016, which compares to 48% and 49%, respectively, in the second quarter of 2015.

• Cash, cash equivalents and investments were $378.7 million as of June 30, 2016.

• DSO was 39 days.

Business Outlook

For the fiscal year ending December 31, 2016, the Company now expects:

• Total revenue to be in the range of $618 to $635 million;

• Net loss in the range of $(0.47) to $(0.44) per share; and

• Non-GAAP net income in the range of $0.31 to $0.34 per share.

Expected non-GAAP net income excludes approximately $42 million related to stock-based compensation expense, approximately $11 million related to the amortization of debt discount and transaction costs, and approximately $5 million related to the amortization of purchased intangible assets. The fully diluted share count for the year is expected to be approximately 73 million for net loss per share, and approximately 75 million shares for non-GAAP net income per share.

The following table reconciles net loss per share to the non-GAAP net income per share range:

	Guidance Range for Year Ending December 31, 2016
	Low			High
Net Loss Per Share	$	(0.47	)	$	(0.44	)
Stock-Based Compensation Expense		0.56			0.56
Amortization of Debt Discount and Transaction Costs		0.07			0.07
Amortization of Purchased Intangible Assets		0.15			0.15
Non-GAAP Measure of Net Income Per Share	$	0.31		$	0.34

Accessing Cepheid’s 2016 Second Quarter Results Conference Call

The Company will host a management presentation at 2 p.m. Pacific Time on Thursday, July 28, 2016 to discuss the results. To access the live webcast, please visit Cepheid’s website at http://ir.cepheid.com. A replay of the webcast will be available shortly following the call and will remain available for at least 90 days.

Summary of Management Presentation

In conjunction with today’s press release, the Company is making a summary of the management presentation immediately available at http://ir.cepheid.com.

About Cepheid

Based in Sunnyvale, California, Cepheid (Nasdaq: CPHD) is a leading molecular diagnostics company that is dedicated to improving healthcare by developing, manufacturing, and marketing accurate yet easy-to-use molecular systems and tests. By automating highly complex and time-consuming manual procedures, the Company’s solutions deliver a better way for institutions of any size to perform sophisticated genetic testing for organisms and genetic-based diseases. Through its strong molecular biology capabilities, the Company is focusing on those applications where accurate, rapid, and actionable test results are needed most, such as managing infectious diseases and cancer. For more information, visit http://www.cepheid.com.

Use of Non-GAAP Measures

The Company has supplemented its reported GAAP financial information, including (1) non-GAAP net income and non-GAAP gross margin that do not include stock-based compensation expense, amortization of debt discount and transaction costs and amortization of purchased intangible assets and (2) revenue metrics presented on a constant currency basis. The presentation of this additional information is not meant to be considered in isolation or as a substitute for results prepared in accordance with U.S. GAAP. The Company’s management uses the non-GAAP information internally to evaluate its ongoing business, continuing operational performance and cash requirements, and believes these non-GAAP measures are useful to investors as they provide a basis for evaluating the Company’s cash requirements and additional insight into the underlying operating results and the Company’s ongoing performance in the ordinary course of its operations.

These non-GAAP measures may be different from non-GAAP measures used by other companies. In addition, these non-GAAP measures are not based on any comprehensive set of accounting rules or principles. The Company believes that non-GAAP measures have limitations in that they do not reflect all of the amounts associated with its results of operations as determined in accordance with U.S. GAAP and that these measures should only be used to evaluate the Company’s results of operations in conjunction with the corresponding GAAP measures.

Non-GAAP Net Income and Non-GAAP Gross Margin

As described above, the Company excludes the following items from one or more of its non-GAAP net income and non-GAAP gross margin when applicable:

Stock-based Compensation Expense. This consists primarily of expenses for stock options and restricted stock under ASC 718 (formerly SFAS 123(R)). The Company excludes stock-based compensation expense from its non-GAAP measures primarily because it is a non-cash expense that the Company does not believe is reflective of ongoing operating results in the period incurred. Further, as the Company applies ASC 718, it believes that it is useful to investors to understand the impact of the application of ASC 718 on its results of operations.

Amortization of Debt Discount and Transaction Costs. The Company incurs amortization of debt discount and transaction costs in connection with the Convertible Senior Notes issued in February 2014. The Company excludes these amounts because these expenses are not reflective of ongoing operating results in the period incurred. These amounts arise from the Company’s issuance of debt and have no direct correlation to the operation of the Company’s business.

Amortization of Purchased Intangible Assets. The Company incurs amortization of purchased intangible assets in connection with acquisitions. The Company excludes these amounts because these expenses are not reflective of ongoing operating results in the period incurred. These amounts arise from the Company’s prior acquisitions and have no direct correlation to the operation of the Company’s business.

Constant Currency

The Company presents certain revenue information in this release on a constant currency basis that excludes the effect of foreign currency rate fluctuations and hedging transactions. The Company calculates constant currency revenue growth by (i) translating current quarter or year-to-date revenues to constant currency revenues using the applicable prior period exchange rates and (ii) excluding any gain or loss from foreign currency hedge contracts that are reported in revenue. The Company believes constant currency revenue growth provides useful supplemental information to investors about the financial performance of the Company’s business and enables a more accurate comparison of financial results between periods, by excluding the impact of currency rate fluctuations and hedging transactions. Investors should be cautioned that the effect of changing foreign currency exchange rates has an actual effect on operating results.

Forward-Looking Statements

This press release contains forward-looking statements that are not purely historical regarding Cepheid’s or its management’s intentions, beliefs, expectations and strategies for the future, including those relating to projected future growth, future revenues, future net loss/income and profitability and future number of fully-diluted shares, including on a non-GAAP basis, strategic investments, market penetration and expansion, development and timing of new products, effectiveness of product development and commercialization efforts and the breadth and speed of test menu expansion, geographic expansion, customer segment expansion and market expansion. Because such statements deal with future events, they are subject to various risks and uncertainties, and actual results could differ materially from the Company’s current expectations. Factors that could cause actual results to differ materially include risks and uncertainties such as those relating to: the Company’s success in increasing commercial and HBDC sales and the effectiveness of its sales personnel; the efficacy of the Company’s on-going cost-reduction and gross margin improvement efforts; the relative mix of commercial and HBDC sales, and relative mix of instrument and test sales; manufacturing costs associated with the ramp-up of new products; the speed and extent of test menu expansion and utilization; the performance and market acceptance of new products, including the Honeycomb module and Omni System and new products related to oncology and genetics; the Company’s ability to sell directly to the smaller hospital market and independent reference laboratory market; the on-going expansion of the Company’s United States sales organization; sales organization productivity and the productivity and effectiveness of the Company’s distributors; the Company’s reliance on distributors in some regions to market, sell and support its products; sufficient customer demand, customer confidence in product availability and available customer budgets for the Company’s products; the Company’s ability to develop new products, complete clinical trials successfully and obtain regulatory clearances in a timely manner for new products; uncertainties related to the FDA regulatory and international regulatory processes; the potential impact of guidelines or recommendations and studies published by various organizations; the level of testing at clinical customer sites, including for Healthcare Associated Infections (HAIs); the Company’s ability to successfully introduce and sell products in clinical markets other than HAIs; long sales cycles and variability in systems placements and reagent pull-through in the Company’s HBDC program; the rate of environmental biothreat testing conducted by the USPS, which will affect the amount of consumable products sold to the USPS; unforeseen supply, development and manufacturing problems; the Company’s ability to manage its inventory levels; the Company’s ability to successfully complete and bring on additional manufacturing lines; the potential need for additional intellectual property licenses for tests and other products and the terms of such licenses; the occurrence of unforeseen expenditures, acquisitions or other transactions; costs associated with litigation; the impact of competitive products and pricing; the impact of foreign currency exchange; the Company’s ability to manage geographically-dispersed operations; the Company’s ability to penetrate new geographic markets and manage the operational risks associated with such new markets; and underlying market conditions worldwide. Readers should also refer to the section entitled “Risk Factors” in Cepheid’s Annual Report on Form 10-K, its most recent Quarterly Report on Form 10-Q, and its other reports filed with the Securities and Exchange Commission.

All forward-looking statements and reasons why results might differ included in this release are made as of the date of this press release, based on information currently available to Cepheid, and Cepheid assumes no obligation to update any such forward-looking statement or reasons why results might differ.

FINANCIAL TABLES FOLLOW

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(in thousands, except per share data)

(unaudited)

	Three Months Ended						Six Months Ended
	June 30,						June 30,
	2016			2015			2016			2015
Revenue	$	146,001		$	132,475		$	290,781		$	265,112
Costs and operating expenses:
Cost of sales		73,235			69,377			145,830			130,578
Collaboration profit sharing		1,284			1,326			1,942			2,593
Research and development		33,592			28,092			63,506			52,078
Sales and marketing		29,874			28,078			58,669			54,014
General and administrative		15,418			16,352			30,473			31,994
Total costs and operating expenses		153,403			143,225			300,420			271,257
Loss from operations		(7,402	)		(10,750	)		(9,639	)		(6,145	)
Other income (expense):
Interest income		799			416			1,459			789
Interest expense		(3,812	)		(3,646	)		(7,577	)		(7,250	)
Foreign currency exchange gain (loss) and other, net		298			(1,496	)		(230	)		(2,440	)
Other expense, net		(2,715	)		(4,726	)		(6,348	)		(8,901	)
Loss before income taxes		(10,117	)		(15,476	)		(15,987	)		(15,046	)
Provision for income taxes		(115	)		(1,254	)		(846	)		(778	)
Net loss	$	(10,232	)	$	(16,730	)	$	(16,833	)	$	(15,824	)
Basic net loss per share	$	(0.14	)	$	(0.23	)	$	(0.23	)	$	(0.22	)
Diluted net loss per share	$	(0.14	)	$	(0.23	)	$	(0.23	)	$	(0.22	)
Shares used in computing basic net loss per share		72,921			71,861			72,754			71,563
Shares used in computing diluted net loss per share		72,921			71,861			72,754			71,563

CEPHEID

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands)

(unaudited)

	June 30,			December 31,
	2016			2015
ASSETS
Current assets:
Cash and cash equivalents	$	100,331		$	112,568
Short-term investments		223,155			210,147
Accounts receivable, net		62,828			66,550
Inventory, net		156,815			148,690
Prepaid expenses and other current assets		23,384			18,515
Total current assets		566,513			556,470
Property and equipment, net		151,999			127,639
Investments		55,184			62,175
Other non-current assets		5,665			4,205
Intangible assets, net		22,383			25,241
Goodwill		39,681			39,681
Total assets	$	841,425		$	815,411
LIABILITIES AND SHAREHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	64,296		$	57,771
Accrued compensation		35,944			39,015
Accrued royalties		4,730			5,469
Accrued and other liabilities		29,483			27,451
Current portion of deferred revenue		15,116			12,778
Total current liabilities		149,569			142,484
Long-term portion of deferred revenue		7,489			5,538
Convertible senior notes, net		287,005			281,627
Other liabilities		19,665			15,779
Total liabilities		463,728			445,428
Shareholders’ equity:
Common stock		454,488			449,704
Additional paid-in capital		282,337			263,429
Accumulated other comprehensive loss, net		(53	)		(908	)
Accumulated deficit		(359,075	)		(342,242	)
Total shareholders’ equity		377,697			369,983
Total liabilities and shareholders’ equity	$	841,425		$	815,411

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

(unaudited)

	Six Months Ended June 30,
	2016			2015
Cash flows from operating activities:
Net loss	$	(16,833	)	$	(15,824	)
Adjustments to reconcile net loss to net cash provided by operating activities:
Depreciation and amortization of property and equipment		15,331			13,435
Amortization of intangible assets		2,858			3,334
Unrealized foreign exchange differences		57			1,338
Amortization of debt discount and transaction costs		5,377			5,044
Impairment of acquired intangible assets, licenses, property and equipment		—			224
Stock-based compensation expense		18,839			15,799
Excess tax benefits from stock-based compensation expense		—			(53	)
Other non-cash items		547			28
Changes in operating assets and liabilities:
Accounts receivable		3,722			(8,949	)
Inventory, net		(8,058	)		(9,267	)
Prepaid expenses and other current assets		(4,252	)		(5,151	)
Other non-current assets		(91	)		(207	)
Accounts payable and other current and non-current liabilities		6,024			9,695
Accrued compensation		(3,071	)		(2,514	)
Deferred revenue		4,288			991
Net cash provided by operating activities		24,738			7,923
Cash flows from investing activities:
Capital expenditures		(34,167	)		(19,308	)
Cost of acquisitions, net		—			(3,000	)
Proceeds from sale of equipment and an intangible asset		44			834
Proceeds from sales of marketable securities and investments		40,730			44,873
Proceeds from maturities of marketable securities and investments		112,313			118,497
Purchases of marketable securities and investments		(158,527	)		(156,401	)
Transfer from (to) restricted cash		(2,049	)		1,328
Net cash used in investing activities		(41,656	)		(13,177	)
Cash flows from financing activities:
Net proceeds from the issuance of common shares and exercise of stock options		4,836			20,592
Excess tax benefits from stock-based compensation expense		—			53
Principal payment of notes payable		(85	)		(80	)
Net cash provided by financing activities		4,751			20,565
Effect of foreign exchange rate change on cash and cash equivalents		(70	)		(1,405	)
Net increase (decrease) in cash and cash equivalents		(12,237	)		13,906
Cash and cash equivalents at beginning of period		112,568			96,663
Cash and cash equivalents at end of period	$	100,331		$	110,569

CEPHEID

RECONCILIATION OF GAAP TO NON-GAAP MEASURES

(in thousands, except per share data)

(unaudited)

	Three Months Ended June 30,						Six Months Ended June 30,
	2016			2015			2016			2015
Revenue, as reported	$	146,001		$	132,475		$	290,781		$	265,112
Foreign currency exchange impact on Q2’16 revenue using Q2’15 rates		(88	)		—			2,481			—
Loss/(benefit) from cash flow hedges		248			(2,391	)		222			(4,585	)
Revenue, at constant currency	$	146,161		$	130,084		$	293,484		$	260,527
Revenue growth, as reported		10	%					10	%
Revenue growth, at constant currency		12	%					13	%
International Revenue, as reported	$	64,799		$	56,288		$	127,189		$	106,620
Foreign currency exchange impact on Q2’16 revenue using Q2’15 rates		(88	)		—			2,481			—
Loss/(benefit) from cash flow hedges		248			(2,391	)		222			(4,585	)
Revenue, at constant currency	$	64,959		$	53,897		$	129,892		$	102,035
International Revenue growth, as reported		15	%					19	%
International Revenue growth, at constant currency		21	%					27	%
Systems and Other Revenue, as reported	$	24,838		$	24,360		$	49,122		$	43,074
Foreign currency exchange impact on Q2’16 revenue using Q2’15 rates		(2	)		—			319			—
Loss/(benefit) from cash flow hedges		(19	)		(515	)		(18	)		(681	)
Systems and Other Revenue, at constant currency	$	24,817		$	23,845		$	49,423		$	42,393
Systems and Other Revenue growth, as reported		2	%					14	%
Systems and Other Revenue growth, at constant currency		4	%					17	%
Reagents and Disposables Revenue, as reported	$	121,163		$	108,115		$	241,659		$	222,038
Foreign currency exchange impact on Q2’16 revenue using Q2’15 rates		(86	)		—			2,162			—
Loss/(benefit) from cash flow hedges		267			(1,876	)		240			(3,904	)
Reagents and Disposables Revenue, at constant currency	$	121,344		$	106,239		$	244,061		$	218,134
Reagents and Disposables Revenue growth, as reported		12	%					9	%
Reagents and Disposables Revenue growth, at constant currency		14	%					12	%
Cost of sales	$	73,235		$	69,377		$	145,830		$	130,578
Stock-based compensation expense		(1,583	)		(1,008	)		(3,098	)		(2,048	)
Amortization of purchased intangible assets		(829	)		(1,024	)		(1,658	)		(2,048	)
Non-GAAP measure of cost of sales	$	70,823		$	67,345		$	141,074		$	126,482
Gross margin on revenue per GAAP		50	%		48	%		50	%		51	%
Gross margin on revenue per Non-GAAP		51	%		49	%		51	%		52	%
Operating expenses	$	78,884		$	72,522		$	152,648		$	138,086
Stock-based compensation expense		(8,272	)		(7,262	)		(15,795	)		(13,779	)
Amortization of purchased intangible assets		(341	)		(382	)		(681	)		(766	)
Non-GAAP measure of operating expenses	$	70,271		$	64,878		$	136,172		$	123,541

CEPHEID

RECONCILIATION OF GAAP TO NON-GAAP MEASURES (continued)

(in thousands, except per share data)

(unaudited)

Loss from operations	$	(7,402	)	$	(10,750	)	$	(9,639	)	$	(6,145	)
Stock-based compensation expense		9,855			8,270			18,893			15,827
Amortization of purchased intangible assets		1,170			1,406			2,339			2,814
Non-GAAP measure of income (loss) from operations	$	3,623		$	(1,074	)	$	11,593		$	12,496
Net loss	$	(10,232	)	$	(16,730	)	$	(16,833	)	$	(15,824	)
Stock-based compensation expense		9,855			8,270			18,893			15,827
Amortization of debt discount and transaction cost		2,710			2,542			5,377			5,044
Amortization of purchased intangible assets		1,170			1,406			2,339			2,814
Non-GAAP measure of net income (loss)	$	3,503		$	(4,512	)	$	9,776		$	7,861
Basic net loss per share	$	(0.14	)	$	(0.23	)	$	(0.23	)	$	(0.22	)
Stock-based compensation expense		0.14			0.12			0.26			0.23
Amortization of debt discount and transaction cost		0.04			0.03			0.07			0.06
Amortization of purchased intangible assets		0.01			0.02			0.03			0.04
Non-GAAP measure of net income (loss) per share	$	0.05		$	(0.06	)	$	0.13		$	0.11
Diluted net loss per share	$	(0.14	)	$	(0.23	)	$	(0.23	)	$	(0.22	)
Stock-based compensation expense		0.14			0.12			0.26			0.23
Amortization of debt discount and transaction cost		0.04			0.03			0.07			0.06
Amortization of purchased intangible assets		0.01			0.02			0.03			0.04
Non-GAAP measure of net income (loss) per share	$	0.05		$	(0.06	)	$	0.13		$	0.11
Shares used in computing basic net income (loss) per share		72,921			71,861			72,754			71,563
Shares used in computing Non-GAAP diluted net income (loss) per share		74,267			71,861			74,143			74,330