10-Q/A

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q/A

Amendment No. 1

(Mark One)
x	QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the quarterly period ended September 30, 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 0-12944

ZYGO CORPORATION
(Exact name of registrant as specified in its charter)
Delaware	06-0864500
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)
Laurel Brook Road, Middlefield, Connecticut	06455
(Address of principal executive offices)	(Zip Code)
(860) 347-8506
Registrant’s telephone number, including area code
N/A
(Former name, former address, and former fiscal year, if changed from last report)

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.

x YES o NO

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 during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).

x YES o NO

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act.

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

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).

o YES x NO

APPLICABLE ONLY TO CORPORATE ISSUERS:

Indicate the number of shares outstanding of each of the issuer’s classes of common stock, as of the latest practicable date.

18,436,393 shares of Common Stock, $.10 Par Value, at September 30, 2012

1

EXPLANATORY NOTE

This Amendment No. 1 (“Amendment No. 1”) to the Quarterly Report on Form 10-Q of Zygo Corporation for the quarter ended September 30, 2012, filed with the U.S. Securities and Exchange Commission (the “SEC”) on November 9, 2012 (the “Original Filing”), is solely for the purpose of furnishing Exhibit 101 (XBRL interactive data) thereto, which was omitted from the Original Filing. Amendment No. 1 revises the exhibit index included in Part II, Item 6 of the Original Filing and Exhibit 101 is included as an exhibit to Amendment No. 1.

Except as described above, Amendment No. 1 does not modify or update the disclosures presented in, or exhibits to, the Original Filing in any way. Those sections of the Original Filing that are unaffected by Amendment No. 1 are not included herein. Amendment No.1 continues to speak as of the date of the Original Filing. Furthermore, Amendment No. 1 does not reflect events occurring after the filing of the Original Filing.

2

PART II - Other Information

Item 6. Exhibits

(a)	Exhibits:
	10.1+§	ZygoLot Share Purchase Agreement, dated September 28, 2012
	31.1+	Certification Pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934, As Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
	31.2+	Certification Pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934, As Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
	32.1+	Certification Pursuant to 18 U.S.C. Section 1350, As Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
	32.2+	Certification Pursuant to 18 U.S.C. Section 1350, As Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
	101.INS*		XBRL Instance Document
	101.SCH*		XBRL Taxonomy Extension
	101.CAL*		XBRL Taxonomy Extension Calculation Linkbase
	101.DEF*		XBRL Taxonomy Extension Definition Linkbase
	101.LAB*		XBRL Taxonomy Extension Label Linkbase
	101.PRE*		XBRL Taxonomy Extension Presentation Linkbase

+          Filed with the Original Filing.

§          Confidential treatment has been requested for certain confidential information contained in this exhibit, marked by brackets. The omitted information has been filed separately with the Securities and Exchange Commission pursuant to Rule 24b-2 of the Securities Exchange Act of 1934, as amended.

*          Pursuant to Rule 406T of Regulation S-T, these interactive data files 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, or Section 18 of the Securities Exchange Act of 1934, as amended, and otherwise are not subject to liability under those sections.

3

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.

Zygo Corporation

(Registrant)

/s/ Chris L. Koliopoulos

Chris L. Koliopoulos

President and Chief Executive Officer

/s/ John P. Jordan

John P. Jordan

Vice President, Chief Financial Officer and Treasurer

Date: November 13, 2012

4

EXHIBIT INDEX

10.1+§	ZygoLot Share Purchase Agreement, dated September 28, 2012
31.1+	Certification Pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934, As Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2+	Certification Pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934, As Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1+	Certification Pursuant to 18 U.S.C. Section 1350, As Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
32.2+	Certification Pursuant to 18 U.S.C. Section 1350, As Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
101.INS*		XBRL Instance Document
101.SCH*		XBRL Taxonomy Extension
101.CAL*		XBRL Taxonomy Extension Calculation Linkbase
101.DEF*		XBRL Taxonomy Extension Definition Linkbase
101.LAB*		XBRL Taxonomy Extension Label Linkbase
101.PRE*		XBRL Taxonomy Extension Presentation Linkbase

+          Filed with the Original Filing.

§          Confidential treatment has been requested for certain confidential information contained in this exhibit, marked by brackets. The omitted information has been filed separately with the Securities and Exchange Commission pursuant to Rule 24b-2 of the Securities Exchange Act of 1934, as amended.

*          Pursuant to Rule 406T of Regulation S-T, these interactive data files 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, or Section 18 of the Securities Exchange Act of 1934, as amended, and otherwise are not subject to liability under those sections.

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Income Taxes (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Components of Income Tax Expense (Benefit) [Table Text Block]

Schedule of components of income tax expense benefit

	Three Months Ended September 30,
	2012					2011
	Amount		Tax Rate %			Amount		Tax Rate %
Income tax expense	$	1,433		32	%	$	786		10	%

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Warranty (Detail) - Schedule of product warranty liability (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Beginning balance	$ 1,188	$ 1,333
Reductions for payments made	(910)	(284)
Changes in accruals related to pre-warranties	232	127
Changes in accruals related to warranties made in the current period	648	104
Ending balance	$ 1,158	$ 1,280

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Share-Based Payments (Detail) - Share-based compensation arrangement by share-based payment award, fair value assumptions and methodology	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Term	7 years 109 days	6 years 219 days
Volatility	59.20%	59.50%
Dividend yield	0.00%	0.00%
Risk-free interest rate	1.20%	1.50%

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Intangible Assets (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Payments To Non Compete Agreement	$ 878
Imputed Interest In NonCompete Agreement	27
Payable To Non Compete Agreement	17
Amortization of Intangible Assets	$ 225	$ 210
Minimum [Member] | Patents [Member]
Finite-Lived Intangible Asset, Useful Life	3 years
Maximum [Member] | Patents [Member]
Finite-Lived Intangible Asset, Useful Life	17 years

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Fair Value Measurements (Detail) - Schedule of fair value assets and liabilities measured on recurring basis (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012	Jun. 30, 2012
Money market funds	$ 19,932	$ 19,931
Trading securities	718	729
Foreign currency hedge	(46)	(3)
Total	20,604	20,657
Fair Value, Inputs, Level 1 [Member]
Money market funds	19,932	19,931
Trading securities	718	729
Total	20,650	20,660
Fair Value, Inputs, Level 2 [Member]
Foreign currency hedge	(46)	(3)
Total	$ (46)	$ (3)

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Inventories (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Inventory, Current [Table Text Block]

Inventories are stated at the lower of cost (determined on a first-in, first-out basis) or market. The following table sets forth the components of inventories at September 30, 2012 and June 30, 2012:

	September 30, 2012		June 30, 2012
Raw materials and manufactured parts	$	12,679	$	12,753
Work in process		11,381		12,031
Finished goods		3,447		2,976
	$	27,507	$	27,760

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Intangible Assets (Detail) - Estimated future amortization expense of intangible assets (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012	Jun. 30, 2012
Estimated Future Amortization Expense
Nine months ending June 30, 2013	$ 665
Fiscal year ending June 30, 2014	807
Fiscal year ending June 30, 2015	796
Fiscal year ending June 30, 2016	576
Fiscal year ending June 30, 2017	445
Fiscal year ending June 30, 2018	322
Thereafter	1,372
Total	$ 4,983	$ 5,198

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Accounting Policies, by Policy (Policies)

3 Months Ended

Sep. 30, 2012

Basis of Presentation and Principles of Consolidation [Policy Text Block]

Basis of Presentation and Principles of Consolidation
Zygo Corporation is a worldwide supplier of optical metrology instruments, precision optics, and electro-optical design and manufacturing services, serving customers in the semiconductor capital equipment, research, defense, life sciences and industrial markets. The accompanying condensed consolidated financial statements include the accounts of Zygo Corporation and its subsidiaries (“Zygo,” “we,” “us,” “our” or “the Company”). The Company follows accounting principles generally accepted in the United States of America (“US GAAP”). Zygo’s reporting currency is the U.S. dollar. The functional currencies of our foreign subsidiaries are their local currency and, as such, amounts included in the condensed consolidated statements of operations are translated at the weighted-average exchange rates for the period. Assets and liabilities are translated at period-end exchange rates, and resulting foreign exchange translation adjustments are recorded in the consolidated balance sheets as a component of accumulated other comprehensive income. All transactions and accounts with the subsidiaries are eliminated from the condensed consolidated financial statements. The results of operations for the three months ended September 30, 2012 are not necessarily indicative of the results to be expected for the full fiscal year.

The condensed consolidated balance sheet at September 30, 2012, the condensed consolidated statements of operations and the condensed consolidated statements of comprehensive income for the three months ended September 30, 2012 and 2011, and the condensed consolidated statements of cash flows for the three months ended September 30, 2012 and 2011 are unaudited but, in management’s opinion, include all adjustments, consisting only of normal recurring accruals, necessary for a fair presentation of the results of the interim periods. The accompanying condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes included in our Annual Report on Form 10-K for the year ended June 30, 2012, including items incorporated by reference therein.

New Accounting Pronouncements, Policy [Policy Text Block]

Adoption of New Accounting Pronouncements
In June 2011, the FASB issued new guidance on the presentation of comprehensive income that requires presentation of the components of net income and other comprehensive income in one continuous statement or in two separate, but consecutive statements. There are no changes to the components that are recognized in net income or other comprehensive income under current US GAAP. The adoption of this guidance in the first quarter of fiscal 2013 did not have a material impact on our condensed consolidated financial statements.

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Inventories (Detail) - Schedule of inventory current (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012	Jun. 30, 2012
Raw materials and manufactured parts	$ 12,679	$ 12,753
Work in process	11,381	12,031
Finished goods	3,447	2,976
	$ 27,507	$ 27,760

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Shareholders' Equity (Detail) - Shareholders' equity and noncontrolling interest (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Equity, beginning of period	$ 173,625
Equity, beginning of period	2,355
Equity, beginning of period	175,980
Net income	2,388	6,469
Net income	606	507
Net income	2,994	6,976
Foreign currency translation effect	408	(971)
Total	2,730	5,705
Total	2,796	5,498
Share based compensation	1,230	1,229
Exercise of employee stock options and related tax effect	704	111
Purchase of subsidiary shares from noncontrolling interest	3,155
Equity, end of period	174,835
Equity, end of period	1,555
Equity, end of period	176,390
Parent [Member]
Equity, beginning of period	173,625	124,720
Net income	2,388	6,469
Foreign currency translation effect	342	(764)
Total	2,730	5,705
Share based compensation	1,615	1,229
Repurchase of restricted stock	(1,062)	(295)
Exercise of employee stock options and related tax effect	704	111
Purchase of subsidiary shares from noncontrolling interest	(2,777)
Equity, end of period	174,835	131,470
Noncontrolling Interest [Member]
Equity, beginning of period	2,355	3,367
Net income	606	507
Foreign currency translation effect	66	(207)
Total	672	300
Dividends attributable to noncontrolling interests	(1,094)	(746)
Purchase of subsidiary shares from noncontrolling interest	(378)
Equity, end of period	1,555	2,921
Total Equity [Member]
Equity, beginning of period	175,980	128,087
Net income	2,994	6,976
Foreign currency translation effect	408	(971)
Total	3,402	6,005
Share based compensation	1,615	1,229
Repurchase of restricted stock	(1,062)	(295)
Exercise of employee stock options and related tax effect	704	111
Dividends attributable to noncontrolling interests	(1,094)	(746)
Purchase of subsidiary shares from noncontrolling interest	(3,155)
Equity, end of period	$ 176,390	$ 134,391

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Segment and Major Customer Information (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Segment Reporting Information, by Segment [Table Text Block]

The following table sets forth segment net revenues, gross profit and gross margin for the three months ended September 30, 2012 and 2011:

	Three Months Ended September 30,
	2012			2011
Metrology Solutions
Net revenues	$	25,878		$	29,842
Gross profit	$	14,335		$	17,370
Gross margin		55	%		58	%
Optical Systems
Net revenues	$	14,328		$	14,150
Gross profit	$	3,158		$	4,247
Gross margin		22	%		30	%
Total
Net revenues	$	40,206		$	43,992
Gross profit	$	17,493		$	21,617
Gross margin		44	%		49	%

Schedule of Revenue from External Customers and Long-Lived Assets, by Geographical Areas [Table Text Block]

The following table sets forth revenues by geographic area:

	Three Months Ended September 30,
	2012		2011
Americas	$	18,863	$	24,293
Japan		6,331		6,786
China		7,538		6,080
Europe		4,822		4,271
Pacific Rim		2,652		2,562
Total	$	40,206	$	43,992

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Property, Plant and Equipment (Detail) - Property plant and equipment (USD $) In Thousands, unless otherwise specified					3 Months Ended				3 Months Ended				3 Months Ended
	Sep. 30, 2012	Jun. 30, 2012	Sep. 30, 2012 Land Improvements [Member]	Jun. 30, 2012 Land Improvements [Member]	Sep. 30, 2012 Building and Building Improvements [Member] Minimum [Member]	Sep. 30, 2012 Building and Building Improvements [Member] Maximum [Member]	Sep. 30, 2012 Building and Building Improvements [Member]	Jun. 30, 2012 Building and Building Improvements [Member]	Sep. 30, 2012 Machinery Equipment And Office Furniture [Member] Minimum [Member]	Sep. 30, 2012 Machinery Equipment And Office Furniture [Member] Maximum [Member]	Sep. 30, 2012 Machinery Equipment And Office Furniture [Member]	Jun. 30, 2012 Machinery Equipment And Office Furniture [Member]	Sep. 30, 2012 Leasehold Improvements [Member] Minimum [Member]	Sep. 30, 2012 Leasehold Improvements [Member] Maximum [Member]	Sep. 30, 2012 Leasehold Improvements [Member]	Jun. 30, 2012 Leasehold Improvements [Member]	Sep. 30, 2012 Construction in Progress [Member]	Jun. 30, 2012 Construction in Progress [Member]
Property, Plant and Equipment, Gross	$ 89,842	$ 89,106	$ 4,030	$ 4,030			$ 24,303	$ 24,228			$ 58,388	$ 58,259			$ 969	$ 964	$ 2,152	$ 1,625
Property, Plant and Equipment, Useful Life					15 years	40 years			3 years	8 years			1 year	5 years
Accumulated depreciation	(56,500)	(55,412)
	$ 33,342	$ 33,694

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Transactions with Shareholder (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011	Jun. 30, 2012
Revenue, Net	$ 40,206	$ 43,992
Accounts Receivable, Net, Current	29,991		31,601
Japan And Subsidiary Of Canon Inc [Member]
Revenue, Net	2,812	4,794
Percentage Of Net Revenues	7.00%	11.00%
Canon Inc [Member] | Trade Accounts Receivable [Member]
Accounts Receivable, Net, Current	$ 1,474		$ 1,604

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Share-Based Payments (Detail) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Share-based Compensation (in Dollars)	$ 1,230	$ 1,229
Employee Service Share-based Compensation, Tax Benefit from Compensation Expense (in Dollars)	$ 398	$ 442
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Weighted Average Grant Date Fair Value (in Dollars per share)	$ 11.49	$ 7.09
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Net of Forfeitures	122,934	221,062
Restricted Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	132,901	115,503
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period, Weighted Average Grant Date Fair Value (in Dollars per share)	$ 19.39	$ 12.26
Prior To January 1, 2011 [Member]
Percentage Of Lapse Rate On Restricted Stock Units Granted To Employees	50.00%
Remaining Percentage Of Lapse Rate On Restricted Stock Units Granted To Employees	50.00%
After January 1, 2011 [Member]
Percentage Of Lapse Rate On Restricted Stock Units Granted To Employees	25.00%

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Earnings Per Share

3 Months Ended

Sep. 30, 2012

Earnings Per Share [Text Block]

Note 2: Earnings Per Share

For the three months ended September 30, 2012 and 2011, outstanding stock options and restricted stock awards for 132,013 shares and 542,335 shares, respectively of the Company’s common stock were excluded from the calculation of diluted earnings per share because they were antidilutive.

The following table sets forth the reconciliation of basic weighted average shares outstanding and diluted weighted average shares outstanding for the periods presented:

	Three Months Ended September 30,
	2012		2011
Basic weighted average shares outstanding		18,341,320		17,799,754
Dilutive effect of stock options and restricted shares		705,784		553,627
Diluted weighted average shares outstanding		19,047,104		18,353,381

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Derivatives and Hedging Activities (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Notional Amount of Foreign Currency Derivative Instruments Not Designated as Hedging Instruments	$ 4,500
Foreign Currency Transaction Gain (Loss), Unrealized	$ 43	$ 39

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Changes in Zygo Corporation's Ownership Interest in Subsidiary (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012
Purchasе of subsidiary sharеs from noncontrolling intеrеst	$ 3,155

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Marketable Securities (Tables)

3 Months Ended

Sep. 30, 2012

Trading Securities (and Certain Trading Assets) [Table Text Block]

The following table sets forth the beginning balance at July 1, 2012 and 2011, gross unrealized gains and losses, contributions, redemptions and fair value of trading securities at September 30, 2012 and 2011:

	Beginning Balance of Fiscal Year		Gross Unrealized Gains		Gross Unrealized Losses			Contri- butions		Redemp- tions			Ending Balance
September 30, 2012 Mutual Fund	$	729	$	32	$	—		$	—	$	(43	)	$	718
September 30, 2011 Mutual Fund	$	980	$	—	$	(101	)	$	—	$	(47	)	$	832

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Changes in Zygo Corporation's Ownership Interest in Subsidiary (Tables)

3 Months Ended

Sep. 30, 2012

Schedule Of Equity Of Changes In Ownership Ineterest [Table Text Block]

The following table discloses the effects on our equity of changes in our ownership interest of ZygoLot, German subsidiary.

	Three Months Ended September 30,
	2012			2011
Net income attributable to Zygo Corporation	$	2,388		$	6,469
Transfers to the noncontrolling interest Decrease in Zygo Corporations paid in capital for purchase of noncontrolling interest		2,749			—
Net transfers to noncontrolling interest		2,749			—
Change from net income attributable to Zygo Corporations shareholders and transfers to noncontrolling interest	$	(361	)	$	6,469

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Intangible Assets (Detail) - Schedule of finite lived intangible assets (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012	Jun. 30, 2012
Intangible assets, gross	$ 9,958	$ 9,948
Accumulated amortization	(4,975)	(4,750)
Total	4,983	5,198
Patents And Trademarks [Member]
Intangible assets, gross	6,944	6,934
Customer Relationships And Technology [Member]
Intangible assets, gross	2,163	2,163
Covenant Not To Compete [Member]
Intangible assets, gross	$ 851	$ 851

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Changes in Zygo Corporation's Ownership Interest in Subsidiary (Detail) - Equity of changes in ownership interest (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Net income attributable to Zygo Corporation	$ 2,388	$ 6,469
Transfers to the noncontrolling interest Decrease in Zygo Corporations paid in capital for purchase of noncontrolling interest	2,749
Net transfers to noncontrolling interest	2,749
Change from net income attributable to Zygo Corporations shareholders and transfers to noncontrolling interest	$ (361)	$ 6,469

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Fair Value Measurements (Tables)

3 Months Ended

Sep. 30, 2012

The following tables provide the assets and liabilities carried at fair value measured on a recurring basis as of September 30, 2012 and June 30, 2012:

				Fair value measurements at September 30, 2012
	Total carrying value at September 30, 2012			Quoted prices in active markets (Level 1)		Significant other observable inputs (Level 2)			Significant unobservable inputs (Level 3)
Money market funds	$	19,932		$	19,932	$	—		$	—
Trading securities		718			718		—			—
Foreign currency hedge		(46	)		—		(46	)		—
Total	$	20,604		$	20,650	$	(46	)	$	—

				Fair value measurements at June 30, 2012
	Total carrying value at June 30, 2012			Quoted prices in active markets (Level 1)		Significant other observable inputs (Level 2)			Significant unobservable inputs (Level 3)
Money market funds	$	19,931		$	19,931	$	—		$	—
Trading securities		729			729		—			—
Foreign currency hedge		(3	)		—		(3	)		—
Total	$	20,657		$	20,660	$	(3	)	$	—

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Share-Based Payments (Tables)

3 Months Ended

Sep. 30, 2012

Share-based Compensation Arrangement by Share-based Payment Award, Fair Value Assumptions and Methodology [Table Text Block]

The table below indicates the key assumptions used in the option valuation calculations for options granted in the periods presented:

	Three Months Ended September 30,
	2012			2011
Term		7.3			6.6
Volatility		59.2	%		59.5	%
Dividend yield		0.0	%		0.0	%
Risk-free interest rate		1.2	%		1.5	%

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Accounting Policies

3 Months Ended

Sep. 30, 2012

Significant Accounting Policies [Text Block]

Note 1: Accounting Policies

Basis of Presentation and Principles of Consolidation
Zygo Corporation is a worldwide supplier of optical metrology instruments, precision optics, and electro-optical design and manufacturing services, serving customers in the semiconductor capital equipment, research, defense, life sciences and industrial markets. The accompanying condensed consolidated financial statements include the accounts of Zygo Corporation and its subsidiaries (“Zygo,” “we,” “us,” “our” or “the Company”). The Company follows accounting principles generally accepted in the United States of America (“US GAAP”). Zygo’s reporting currency is the U.S. dollar. The functional currencies of our foreign subsidiaries are their local currency and, as such, amounts included in the condensed consolidated statements of operations are translated at the weighted-average exchange rates for the period. Assets and liabilities are translated at period-end exchange rates, and resulting foreign exchange translation adjustments are recorded in the consolidated balance sheets as a component of accumulated other comprehensive income. All transactions and accounts with the subsidiaries are eliminated from the condensed consolidated financial statements. The results of operations for the three months ended September 30, 2012 are not necessarily indicative of the results to be expected for the full fiscal year.

The condensed consolidated balance sheet at September 30, 2012, the condensed consolidated statements of operations and the condensed consolidated statements of comprehensive income for the three months ended September 30, 2012 and 2011, and the condensed consolidated statements of cash flows for the three months ended September 30, 2012 and 2011 are unaudited but, in management’s opinion, include all adjustments, consisting only of normal recurring accruals, necessary for a fair presentation of the results of the interim periods. The accompanying condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes included in our Annual Report on Form 10-K for the year ended June 30, 2012, including items incorporated by reference therein.

Adoption of New Accounting Pronouncements
In June 2011, the FASB issued new guidance on the presentation of comprehensive income that requires presentation of the components of net income and other comprehensive income in one continuous statement or in two separate, but consecutive statements. There are no changes to the components that are recognized in net income or other comprehensive income under current US GAAP. The adoption of this guidance in the first quarter of fiscal 2013 did not have a material impact on our condensed consolidated financial statements.

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Receivables (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Accounts, Notes, Loans and Financing Receivable [Table Text Block]

The following table sets forth the components of accounts receivable at September 30, 2012 and June 30, 2012:

	September 30, 2012			June 30, 2012
Trade	$	30,528		$	32,261
Other		162			100
		30,690			32,361
Allowance for doubtful accounts		(699	)		(760	)
	$	29,991		$	31,601

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Earnings Per Share (Detail)	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	132,013	542,335

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Warranty (Detail)	3 Months Ended
	Sep. 30, 2012
Standard Product Warranty Description	A limited warranty is provided on our products for periods ranging from 3 to 24 months, and allowances for estimated warranty costs are recorded during the period of sale. The determination of such allowances requires management to make estimates of product return rates and expected costs to repair or replace products under warranty. If actual return rates or repair and replacement costs, or both, differ significantly from management estimates, adjustments to the expense will be required

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CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Net revenue	$ 40,206	$ 43,992
Cost of goods sold	22,713	22,375
Gross profit	17,493	21,617
Selling, general and administrative expenses	8,521	9,463
Research, development and engineering expenses	4,581	4,062
Operating profit	4,391	8,092
Other income (expense)
Miscellaneous income (expense), net	36	(330)
Total other income (expense)	36	(330)
Income before income taxes, including noncontrolling interests	4,427	7,762
Income tax expense	(1,433)	(786)
Net income including noncontrolling interests	2,994	6,976
Less: Net income attributable to noncontrolling interests	606	507
Net income attributable to Zygo Corporation	$ 2,388	$ 6,469
Earnings per share attributable to Zygo Corporation
Basic earnings per share (in Dollars per share)	$ 0.13	$ 0.36
Diluted earnings per share (in Dollars per share)	$ 0.13	$ 0.35
Weighted average shares outstanding
Basic shares (in Shares)	18,341,320	17,799,754
Diluted shares (in Shares)	19,047,104	18,353,381

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Marketable Securities (Detail) - Schedule of trading securities (Mutual Fund [Member], USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Mutual Fund [Member]
Beginning Balance of Fiscal Year	$ 729	$ 980
Gross Unrealized Gains	32
Gross Unrealized Losses		(101)
Redemptions	(43)	(47)
Ending Balance	$ 718	$ 832

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Cash provided by operating activities:
Net income including noncontrolling interests	$ 2,994	$ 6,976
Adjustments to reconcile net income to cash provided by operating activities from continuing operations:
Depreciation and amortization	1,400	1,452
Loss on disposal of assets		21
Deferred income taxes	(1,397)
Provision for doubtful accounts	(62)	(90)
Compensation cost related to share-based payment arrangements	1,230	1,229
Excess tax benefits from share-based payment arrangements		(2)
Other	(133)	38
Changes in operating accounts:
Receivables	1,880	(1,850)
Inventories	477	1,645
Prepaid expenses and other current assets	292	(128)
Revenue recognized in excess of billings on uncompleted contracts	(2,102)
Accounts payable, accrued expenses and taxes payable	(4,314)	(4,262)
Net cash provided by operating activities from continuing operations	265	5,029
Net cash used for operating activities from discontinued operations		(141)
Cash used for investing activities:
Additions to property, plant and equipment	(1,104)	(390)
Purchase of marketable securities		(999)
Additions to intangibles	(11)	(25)
Investments and acquisitions	(3,155)
Proceeds from the sale and maturity of marketable securities	43	1,047
Net cash used for investing activities	(4,227)	(367)
Cash used for financing activities:
Dividend payment to noncontrolling interest	(1,094)	(746)
Excess tax benefits from share-based payment arrangements		2
Repurchase of restricted stock	(1,062)	(295)
Exercise of employee stock options	704	111
Net cash used for financing activities	(1,452)	(928)
Effect of exchange rate changes on cash and cash equivalents	195	(696)
Net increase (decrease) in cash and cash equivalents	(5,219)	2,897
Cash and cash equivalents, beginning of period	84,053	60,039
Cash and cash equivalents, end of period	$ 78,834	$ 62,936

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Segment and Major Customer Information (Detail) - Schedule of segment reporting information by segment (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Net revenues	$ 40,206	$ 43,992
Gross profit	17,493	21,617
Gross margin	44.00%	49.00%
Metrology Solutions [Member]
Net revenues	25,878	29,842
Gross profit	14,335	17,370
Gross margin	55.00%	58.00%
Optical Systems [Member]
Net revenues	14,328	14,150
Gross profit	$ 3,158	$ 4,247
Gross margin	22.00%	30.00%

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Warranty (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Product Warranty Liability [Table Text Block]

The following table is a reconciliation of the beginning and ending balances of the accrued warranty liability, which is included in “Other accrued expenses” in the condensed consolidated balance sheets:

	Three Months Ended September 30,
	2012			2011
Beginning balance	$	1,188		$	1,333
Reductions for payments made		(910	)		(284	)
Changes in accruals related to pre-warranties		232			127
Changes in accruals related to warranties made in the current period		648			104
Ending balance	$	1,158		$	1,280

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Income Taxes (Detail) - Schedule of components of income tax expense benefit (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Income tax expense (in Dollars)	$ 1,433	$ 786
Income tax expense	32.00%	10.00%

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Derivatives and Hedging Activities

3 Months Ended

Sep. 30, 2012

Derivative Instruments and Hedging Activities Disclosure [Text Block]

Note 15: Derivatives and Hedging Activities

We enter into foreign currency forward contracts to reduce the impact of adverse fluctuations on income associated with foreign currency exchange rate changes. We do not enter into any derivative transactions for speculative purposes. The contracts are not designated as cash flow, fair value, or net investment hedges as defined under authoritative guidance on accounting for derivative instruments and hedging activities. These contracts are marked-to-market with changes in fair value recorded in the condensed consolidated statements of operations in “Miscellaneous income.” The contracts are entered into for periods consistent with the expected currency transaction exposures, generally three to six months. Any gains and losses on the fair value of these contracts are expected to substantially offset corresponding losses and gains on the underlying transactions.

As of September 30, 2012, there were thirteen currency contracts outstanding involving our Japanese operation with notional amounts aggregating $4,500. These foreign currency hedges are not designated as hedging instruments. For the three months ended September 30, 2012 and 2011, we recognized net unrealized losses of $43 and net unrealized gains of $39, respectively, from foreign currency forward contracts. These unrealized losses and gains are essentially offset by foreign exchange gains and losses on intercompany balances recorded by our subsidiaries and are recorded in miscellaneous income on our condensed consolidated statements of operations.

The following table summarizes the fair value of derivative instruments as of September 30, 2012 and June 30, 2012:

	Derivatives not designated as hedging instruments			Balance Sheet Location
September 30, 2012		Number of foreign exchange contracts:	13	Other accrued liabilities	$46
June 30, 2012		Number of foreign exchange contracts:	9	Prepaid expenses and other current assets	$14
				Other accrued expenses	$17

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Intangible Assets (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Finite-Lived Intangible Assets [Table Text Block]

The following table sets forth the components of intangible assets, as of September 30, 2012 and June 30, 2012:

	September 30, 2012			June 30, 2012
Patents	$	6,944		$	6,934
Customer relationships and technology		2,163			2,163
Covenant not-to-compete		851			851
		9,958			9,948
Accumulated amortization		(4,975	)		(4,750	)
Total	$	4,983		$	5,198

Schedule of Finite-Lived Intangible Assets, Future Amortization Expense [Table Text Block]

Based on the carrying amount of the intangible assets as of September 30, 2012, the estimated future amortization expense is as follows:

	Estimated Future Amortization Expense
Nine months ending June 30, 2013		$	665
Fiscal year ending June 30, 2014			807
Fiscal year ending June 30, 2015			796
Fiscal year ending June 30, 2016			576
Fiscal year ending June 30, 2017			445
Fiscal year ending June 30, 2018			322
Thereafter			1,372
Total		$	4,983

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Commitments and Contingencies

3 Months Ended

Sep. 30, 2012

Commitments and Contingencies Disclosure [Text Block]

Note 17: Commitments and Contingencies

From time to time we are subject to certain legal proceedings and claims that arise in the normal course of business.

We are aware of certain levels of environmental contamination that are below reportable levels on one of our properties. In addition, we are aware of certain contamination on an adjacent property that we formerly owned. The future effect of environmental matters, including potential liabilities, is often difficult to estimate. At this time, we are unable to determine or reasonably estimate the amount of costs, if any, that we might incur or for which we may potentially be responsible. We will record a reserve for the exposure related to the environmental contamination when and if it is both probable that a liability has been incurred and the amount of any liability can be reasonably estimated, whether or not a claim has been asserted.

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Parentheticals) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Net cash paid for income taxes	$ 1,206	$ 1,011
Purchases of property, plant and equipment	$ 275	$ 67

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CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Net income attributable to Zygo Corporation	$ 2,388	$ 6,469
Other comprehensive income (loss)
Foreign currency translation adjustment	408	(971)
Comprehensive income	2,796	5,498
Less: Comprehensive income attributable to noncontrolling interests	66	(207)
Comprehensive income attribuatable to Zygo Corporation	$ 2,730	$ 5,705

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Property, Plant and Equipment

3 Months Ended

Sep. 30, 2012

Property, Plant and Equipment Disclosure [Text Block]

Note 10: Property, Plant and Equipment

Property, plant and equipment are stated at cost less impairments. Maintenance and repairs are charged to expense as incurred. Management evaluates, on an ongoing basis, the carrying value of property, plant and equipment and makes adjustments when impairments are identified. Depreciation is based on the estimated useful lives of the various classes of assets and is computed using the straight-line method. The following table sets forth the components of property, plant and equipment at September 30, 2012 and June 30, 2012:

	September 30, 2012			June 30, 2012			Estimated Useful Life (Years)
								Minimum	Maximum
Land and improvements	$	4,030		$	4,030		—
Building and improvements		24,303			24,228			15	40
Machinery, equipment and office furniture		58,388			58,259			3	8
Leasehold improvements		969			964			1	5
Construction in progress		2,152			1,625		—
		89,842			89,106
Accumulated depreciation		(56,500	)		(55,412	)
	$	33,342		$	33,694

Depreciation expense was $1,175 and $1,243 for the three months ended September 30, 2012 and 2011, respectively.

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Document And Entity Information	3 Months Ended
	Sep. 30, 2012
Document and Entity Information [Abstract]
Entity Registrant Name	ZYGO CORP
Document Type	10-Q
Current Fiscal Year End Date	--06-30
Entity Common Stock, Shares Outstanding	18,436,393
Amendment Flag	false
Entity Central Index Key	0000730716
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Accelerated Filer
Entity Well-known Seasoned Issuer	No
Document Period End Date	Sep. 30, 2012
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q1

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Warranty

3 Months Ended

Sep. 30, 2012

Product Warranty Disclosure [Text Block]

Note 11: Warranty

A limited warranty is provided on our products for periods ranging from 3 to 24 months, and allowances for estimated warranty costs are recorded during the period of sale. The determination of such allowances requires management to make estimates of product return rates and expected costs to repair or replace products under warranty. If actual return rates or repair and replacement costs, or both, differ significantly from management estimates, adjustments to the expense will be required.

The following table is a reconciliation of the beginning and ending balances of the accrued warranty liability, which is included in “Other accrued expenses” in the condensed consolidated balance sheets:

	Three Months Ended September 30,
	2012			2011
Beginning balance	$	1,188		$	1,333
Reductions for payments made		(910	)		(284	)
Changes in accruals related to pre-warranties		232			127
Changes in accruals related to warranties made in the current period		648			104
Ending balance	$	1,158		$	1,280

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CONDENSED CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012	Jun. 30, 2012
Current assets:
Cash and cash equivalents	$ 78,834	$ 84,053
Receivables, net of allowance for doubtful accounts of $699 and $760, respectively	29,991	31,601
Inventories	27,507	27,760
Prepaid expenses and other current assets	2,567	2,851
Revenue recognized in excess of billings on uncompleted contracts	4,473	2,371
Deferred income taxes	9,788	8,004
Total current assets	153,160	156,640
Marketable securities	718	729
Property, plant and equipment, net	33,342	33,694
Deferred income taxes	13,768	13,760
Intangible assets, net	4,983	5,198
Total assets	205,971	210,021
Current liabilities:
Accounts payable	8,061	9,613
Progress payments and deferred revenue	3,742	5,482
Accrued salaries and wages	2,980	6,198
Other accrued expenses	7,324	7,234
Income taxes payable	648	416
Total current liabilities	22,755	28,943
Deferred income taxes	2,580	2,580
Other long-term liabilities	4,246	2,518
Total Liabilities	29,581	34,041
Commitments and contingencies
Equity:
Common stock, $0.10 par value per share: 40,000,000 shares authorized;20,752,552 shares issued (20,499,861 at June 30, 2012);18,436,393 shares outstanding (18,239,941 at June 30, 2012)	2,075	2,050
Additional paid-in capital	175,822	176,305
Retained earnings	24,641	22,253
Accumulated other comprehensive income (loss):
Currency translation effects	156	(186)
Treasury stock, at cost, 2,316,159 shares (2,259,920 at June 30, 2012)	(27,859)	(26,797)
Total shareholders’ equity - Zygo Corporation	174,835	173,625
Noncontrolling interests	1,555	2,355
Total equity	176,390	175,980
Total liabilities and equity	$ 205,971	$ 210,021

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Marketable Securities

3 Months Ended

Sep. 30, 2012

Investments in Debt and Marketable Equity Securities (and Certain Trading Assets) Disclosure [Text Block]

Note 5: Marketable Securities

Marketable securities consisted of a mutual fund investment consisting primarily of corporate securities as of September 30, 2012 which is classified as a trading security. Dividend and interest income is recognized when earned. Straight-line amortization related to discounts and premiums on the purchase of marketable securities is recorded in interest income. Realized gains and losses are included in net income and are derived using the specific identification method for determining the cost of securities sold.

Trading securities consisted of a mutual fund investment corresponding to elections made in our deferred compensation program. In December 2010, we began quarterly distributions in accordance with the deferred compensation program agreement. The following table sets forth the beginning balance at July 1, 2012 and 2011, gross unrealized gains and losses, contributions, redemptions and fair value of trading securities at September 30, 2012 and 2011:

	Beginning Balance of Fiscal Year		Gross Unrealized Gains		Gross Unrealized Losses			Contri- butions		Redemp- tions			Ending Balance
September 30, 2012 Mutual Fund	$	729	$	32	$	—		$	—	$	(43	)	$	718
September 30, 2011 Mutual Fund	$	980	$	—	$	(101	)	$	—	$	(47	)	$	832

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Changes in Zygo Corporation's Ownership Interest in Subsidiary

3 Months Ended

Sep. 30, 2012

Changes In Ownership Interest In Subsidiary [Text Block]

Note 4: Changes in Zygo Corporation’s Ownership Interest in Subsidiary

Zygo Corporation purchased the outstanding noncontrolling interest in our German subsidiary for $3,155. The following table discloses the effects on our equity of changes in our ownership interest of ZygoLot, German subsidiary.

	Three Months Ended September 30,
	2012			2011
Net income attributable to Zygo Corporation	$	2,388		$	6,469
Transfers to the noncontrolling interest Decrease in Zygo Corporations paid in capital for purchase of noncontrolling interest		2,749			—
Net transfers to noncontrolling interest		2,749			—
Change from net income attributable to Zygo Corporations shareholders and transfers to noncontrolling interest	$	(361	)	$	6,469

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Income Taxes

3 Months Ended

Sep. 30, 2012

Income Tax Disclosure [Text Block]

Note 16: Income Taxes

	Three Months Ended September 30,
	2012					2011
	Amount		Tax Rate %			Amount		Tax Rate %
Income tax expense	$	1,433		32	%	$	786		10	%

Income tax expense for the three months ended September 30, 2012 related primarily to United States (“U.S.”) Federal, state and foreign income tax expense and includes a tax benefit of $398 to correct an error in recording deferred tax asset balances as of June 30, 2012 relating to fixed assets and foreign tax credits. Income tax expense for the three months ended September 30, 2011 related primarily to foreign and state income tax expense; there was no U.S. federal tax expense during that period due to the valuation allowance on net operating loss carryforwards. The Company is subject to U.S. federal income tax as well as income tax in multiple state and foreign jurisdictions. The Company is no longer subject to U.S. federal income tax audit or tax adjustments for years prior to June 30, 2007, except to the extent there are NOLs and credits arising from any of those years. Those years are subject to audit at the time the NOL or credit is utilized. The Company is no longer subject to state and foreign income tax audit or tax adjustments for years prior to June 30, 2006.

In the normal course of business, we analyze for uncertain tax positions and adjust our unrecognized tax benefits or liabilities accordingly. For the three months ended September 30, 2012, we recognized an additional liability of $190 for changes in tax positions. We are not aware of any tax positions that would create a material adjustment to the unrecognized tax benefits during the next twelve months.

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Intangible Assets

3 Months Ended

Sep. 30, 2012

Intangible Assets Disclosure [Text Block]

Note 12: Intangible Assets

Intangible assets includes patents, customer relationships and technology and a covenant not-to-compete. The cost of patents and customer relationships and technology is amortized on a straight-line basis over estimated useful lives ranging from 3-17 years. We entered into a non-compete agreement with a former officer and director of the Company effective February 28, 2009. The agreement calls for payments over a four year period of declining amounts totaling $878, which includes $27 of imputed interest. As of September 30, 2012, current liabilities includes $17 related to the payments under this agreement. We amortize the value of the non-compete over four years on a declining-balance method.

The following table sets forth the components of intangible assets, as of September 30, 2012 and June 30, 2012:

	September 30, 2012			June 30, 2012
Patents	$	6,944		$	6,934
Customer relationships and technology		2,163			2,163
Covenant not-to-compete		851			851
		9,958			9,948
Accumulated amortization		(4,975	)		(4,750	)
Total	$	4,983		$	5,198

Amortization expense related to intangibles was $225 and $210 for the three months ended September 30, 2012 and 2011, respectively. This amortization expense related to intangible assets is included in “Cost of goods sold” and “Selling, general and administrative expenses” in the condensed consolidated statements of operations.

Based on the carrying amount of the intangible assets as of September 30, 2012, the estimated future amortization expense is as follows:

	Estimated Future Amortization Expense
Nine months ending June 30, 2013		$	665
Fiscal year ending June 30, 2014			807
Fiscal year ending June 30, 2015			796
Fiscal year ending June 30, 2016			576
Fiscal year ending June 30, 2017			445
Fiscal year ending June 30, 2018			322
Thereafter			1,372
Total		$	4,983

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Receivables

3 Months Ended

Sep. 30, 2012

Loans, Notes, Trade and Other Receivables Disclosure [Text Block]

Note 8: Receivables

The following table sets forth the components of accounts receivable at September 30, 2012 and June 30, 2012:

	September 30, 2012			June 30, 2012
Trade	$	30,528		$	32,261
Other		162			100
		30,690			32,361
Allowance for doubtful accounts		(699	)		(760	)
	$	29,991		$	31,601

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Segment and Major Customer Information (Detail) - Schedule of revenues by geographic area (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Sales Revenue Net	$ 40,206	$ 43,992
Americas [Member]
Sales Revenue Net	18,863	24,293
Japan [Member]
Sales Revenue Net	6,331	6,786
China [Member]
Sales Revenue Net	7,538	6,080
Europe [Member]
Sales Revenue Net	4,822	4,271
Pacific Rim [Member]
Sales Revenue Net	$ 2,652	$ 2,562

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Fair Value Measurements

3 Months Ended

Sep. 30, 2012

Fair Value Disclosures [Text Block]

Note 6. Fair Value Measurements

Fair value measurement disclosures utilize a valuation hierarchy for determining the grouping of the inputs used. This hierarchy prioritizes the inputs into three broad levels. Level 1 inputs are quoted prices (unadjusted) in active markets for identical assets or liabilities. Level 2 inputs are quoted prices for similar assets and liabilities in active markets or inputs that are observable for the asset or liability, either directly or indirectly through market corroboration, for substantially the full term of the financial instrument. Level 3 inputs are unobservable inputs based on management’s assumptions used to measure assets and liabilities at fair value. A financial asset or liabilities classification within the hierarchy is determined based on the lowest level input that is significant to the fair value measurement.

When available, the Company uses quoted market prices to determine the fair value of its assets and liabilities included in Level 1. When quoted market prices are unobservable, the Company uses quotes from independent pricing vendors based on recent trading activity and other relevant information. The carrying value of other financial instruments, including cash, accounts receivable, accounts payable and accrued liabilities, approximates fair value due to their short maturities.

The following tables provide the assets and liabilities carried at fair value measured on a recurring basis as of September 30, 2012 and June 30, 2012:

Assets and Liabilities Measured at Fair Value:

				Fair value measurements at September 30, 2012
	Total carrying value at September 30, 2012			Quoted prices in active markets (Level 1)		Significant other observable inputs (Level 2)			Significant unobservable inputs (Level 3)
Money market funds	$	19,932		$	19,932	$	—		$	—
Trading securities		718			718		—			—
Foreign currency hedge		(46	)		—		(46	)		—
Total	$	20,604		$	20,650	$	(46	)	$	—

Assets and Liabilities Measured at Fair Value:

				Fair value measurements at June 30, 2012
	Total carrying value at June 30, 2012			Quoted prices in active markets (Level 1)		Significant other observable inputs (Level 2)			Significant unobservable inputs (Level 3)
Money market funds	$	19,931		$	19,931	$	—		$	—
Trading securities		729			729		—			—
Foreign currency hedge		(3	)		—		(3	)		—
Total	$	20,657		$	20,660	$	(3	)	$	—

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Share-Based Payments

3 Months Ended

Sep. 30, 2012

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

Note 7: Share-Based Payments

We recorded share-based compensation expense for the three months ended September 30, 2012 and 2011 of $1,230 and $1,229, respectively, with related tax benefits of $398 and $442, respectively.

Stock Options
We use the Black-Scholes option-pricing model to calculate the fair value of stock option awards. The key assumptions for this valuation method include the expected term of the option, stock price volatility, risk-free interest rate, dividend yield and exercise price. Many of these assumptions are judgmental and highly sensitive in the determination of compensation expense. Under the assumptions indicated below, the weighted-average fair value of stock option grants for the three months ended September 30, 2012 and 2011 was $11.49 and $7.09, respectively. During the three months ended September 30, 2012 and 2011, we issued stock options for an aggregate of 122,934 and 221,062 shares of common stock, respectively.

The table below indicates the key assumptions used in the option valuation calculations for options granted in the periods presented:

	Three Months Ended September 30,
	2012			2011
Term		7.3			6.6
Volatility		59.2	%		59.5	%
Dividend yield		0.0	%		0.0	%
Risk-free interest rate		1.2	%		1.5	%

Restricted Stock
Our share-based compensation expense also includes the effects of the issuance of restricted stock units. The compensation expense related to restricted stock awards is determined based on the market price of our stock at the date of grant applied to the total number of shares that are anticipated to fully vest, which is then amortized over the expected term. During the three months ended September 30, 2012 and 2011, an aggregate of 132,901 and 115,503 shares, respectively, of restricted stock units were issued at a weighted average stock price at date of grant of $19.39 and $12.26, respectively. Generally, the restrictions on the restricted stock units granted to employees prior to January 1, 2011 lapse at a rate of 50% after three years and the remaining 50% after the fourth year. Restrictions on restricted stock units granted to employees after January 1, 2011 lapse at a rate of 25% each year.

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Inventories

3 Months Ended

Sep. 30, 2012

Inventory Disclosure [Text Block]

Note 9: Inventories

Inventories are stated at the lower of cost (determined on a first-in, first-out basis) or market. The following table sets forth the components of inventories at September 30, 2012 and June 30, 2012:

	September 30, 2012		June 30, 2012
Raw materials and manufactured parts	$	12,679	$	12,753
Work in process		11,381		12,031
Finished goods		3,447		2,976
	$	27,507	$	27,760

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Income Taxes (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012
Tax Benefit To Correct Error In Deferred Tax Asset	$ 398
Additional Liability for Changes In Tax Positions	$ 190

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Derivatives and Hedging Activities (Detail) - Schedule of foreign exchange contracts statement of financial position (USD $) In Thousands, unless otherwise specified	3 Months Ended	12 Months Ended
	Sep. 30, 2012	Jun. 30, 2012
Other Accrued Liabilities [Member]
Number of foreign exchange contracts	13
Balance Sheet Location	Other accrued liabilities	Other accrued expenses
Fair value of derivative instruments	$ 46	$ 17
Prepaid Expense And Other [Member]
June 30, 2012		9
June 30, 2012		Prepaid expenses and other current assets
June 30, 2012		$ 14

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Property, Plant and Equipment (Tables)

3 Months Ended

Sep. 30, 2012

Property, Plant and Equipment [Table Text Block]

The following table sets forth the components of property, plant and equipment at September 30, 2012 and June 30, 2012:

	September 30, 2012			June 30, 2012			Estimated Useful Life (Years)
								Minimum	Maximum
Land and improvements	$	4,030		$	4,030		—
Building and improvements		24,303			24,228			15	40
Machinery, equipment and office furniture		58,388			58,259			3	8
Leasehold improvements		969			964			1	5
Construction in progress		2,152			1,625		—
		89,842			89,106
Accumulated depreciation		(56,500	)		(55,412	)
	$	33,342		$	33,694

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Property, Plant and Equipment (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Depreciation	$ 1,175	$ 1,243

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Transactions with Shareholder

3 Months Ended

Sep. 30, 2012

Related Party Transactions Disclosure [Text Block]

Note 14: Transactions with Shareholder

Revenues from Canon Inc., a shareholder, and Canon Sales Co., Inc., a distributor of certain of our products in Japan and a subsidiary of Canon Inc. (collectively referred to as “Canon”), amounted to $2,812 and $4,794 (7% and 11% of net revenues, respectively) for the three months ended September 30, 2012 and 2011, respectively. Selling prices of products sold to Canon are based, generally, on the terms customarily given to distributors. At September 30, 2012 and June 30, 2012, there were, in the aggregate, $1,474 and $1,604, respectively, of trade accounts receivable from Canon.

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Earnings Per Share (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Weighted Average Number of Shares [Table Text Block]

The following table sets forth the reconciliation of basic weighted average shares outstanding and diluted weighted average shares outstanding for the periods presented:

	Three Months Ended September 30,
	2012		2011
Basic weighted average shares outstanding		18,341,320		17,799,754
Dilutive effect of stock options and restricted shares		705,784		553,627
Diluted weighted average shares outstanding		19,047,104		18,353,381

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Receivables (Detail) - Schedule of accounts notes receivable (USD $) In Thousands, unless otherwise specified	Sep. 30, 2012	Jun. 30, 2012
Receivables	$ 30,690	$ 32,361
Allowance for doubtful accounts	(699)	(760)
	29,991	31,601
Trade Accounts Receivable [Member]
Receivables	30,528	32,261
Other Receiveable [Member]
Receivables	$ 162	$ 100

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Earnings Per Share (Detail) - Earnings per share basic earnings per share (EPS) is computed based on the weighted average number	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Basic weighted average shares outstanding	18,341,320	17,799,754
Dilutive effect of stock options and restricted shares	705,784	553,627
Diluted weighted average shares outstanding	19,047,104	18,353,381

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CONDENSED CONSOLIDATED BALANCE SHEETS (Parentheticals) (USD $) In Thousands, except Share data, unless otherwise specified	Sep. 30, 2012	Jun. 30, 2012
Allowance for doubtful accounts (in Dollars)	$ 699	$ 760
Common stock, par value (in Dollars per share)	$ 0.10	$ 0.10
Common stock, shares authorized	40,000,000	40,000,000
Common stock, shares issued	20,752,552	20,499,861
Common stock, shares outstanding	18,436,393	18,239,941
Treasury stock, shares	2,316,159	2,259,920

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Shareholders' Equity

3 Months Ended

Sep. 30, 2012

Stockholders' Equity Note Disclosure [Text Block]

Note 3: Shareholders’ Equity

The following table sets forth shareholders’ equity and noncontrolling interest for the three months ended September 30, 2012 and 2011:

	Three Months Ended September 30,
	2012									2011
	Shareholders’ Equity Zygo Corp.			Non- Controlling Interests			Total Equity			Shareholders’ Equity Zygo Corp.			Non- Controlling Interests			Total Equity
Equity, beginning of period	$	173,625		$	2,355		$	175,980		$	124,720		$	3,367		$	128,087
Net income		2,388			606			2,994			6,469			507			6,976
Foreign currency translation effect		342			66			408			(764	)		(207	)		(971	)
Total		2,730			672			3,402			5,705			300			6,005
Share based compensation		1,615			—			1,615			1,229			—			1,229
Repurchase of restricted stock		(1,062	)		—			(1,062	)		(295	)		—			(295	)
Exercise of employee stock options and related tax effect		704			—			704			111			—			111
Dividends attributable to noncontrolling interests		—			(1,094	)		(1,094	)		—			(746	)		(746	)
Purchase of subsidiary shares from noncontrolling interest		(2,777	)		(378	)		(3,155	)		—			—			—
Equity, end of period	$	174,835		$	1,555		$	176,390		$	131,470		$	2,921		$	134,391

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Segment and Major Customer Information (Detail)	3 Months Ended
	Sep. 30, 2012	Sep. 30, 2011
Customer One [Member]
Entity-Wide Revenue, Major Customer, Percentage	7.00%	11.00%
Customer Two [Member]
Entity-Wide Revenue, Major Customer, Percentage	12.00%	10.00%

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Shareholders' Equity (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Stockholders Equity [Table Text Block]

The following table sets forth shareholders’ equity and noncontrolling interest for the three months ended September 30, 2012 and 2011:

	Three Months Ended September 30,
	2012									2011
	Shareholders’ Equity Zygo Corp.			Non- Controlling Interests			Total Equity			Shareholders’ Equity Zygo Corp.			Non- Controlling Interests			Total Equity
Equity, beginning of period	$	173,625		$	2,355		$	175,980		$	124,720		$	3,367		$	128,087
Net income		2,388			606			2,994			6,469			507			6,976
Foreign currency translation effect		342			66			408			(764	)		(207	)		(971	)
Total		2,730			672			3,402			5,705			300			6,005
Share based compensation		1,615			—			1,615			1,229			—			1,229
Repurchase of restricted stock		(1,062	)		—			(1,062	)		(295	)		—			(295	)
Exercise of employee stock options and related tax effect		704			—			704			111			—			111
Dividends attributable to noncontrolling interests		—			(1,094	)		(1,094	)		—			(746	)		(746	)
Purchase of subsidiary shares from noncontrolling interest		(2,777	)		(378	)		(3,155	)		—			—			—
Equity, end of period	$	174,835		$	1,555		$	176,390		$	131,470		$	2,921		$	134,391

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Derivatives and Hedging Activities (Tables)

3 Months Ended

Sep. 30, 2012

Schedule of Foreign Exchange Contracts, Statement of Financial Position [Table Text Block]

The following table summarizes the fair value of derivative instruments as of September 30, 2012 and June 30, 2012:

	Derivatives not designated as hedging instruments			Balance Sheet Location
September 30, 2012		Number of foreign exchange contracts:	13	Other accrued liabilities	$46
June 30, 2012		Number of foreign exchange contracts:	9	Prepaid expenses and other current assets	$14
				Other accrued expenses	$17

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Segment and Major Customer Information

3 Months Ended

Sep. 30, 2012

Segment Reporting Disclosure [Text Block]

Note 13: Segment and Major Customer Information

Our business is organized into two operating divisions – Metrology Solutions (Metrology Solutions segment) and Optical Systems (Optical Systems segment). Consistent with our business structure, we report our segments as Metrology Solutions and Optical Systems. Our Metrology Solutions segment includes 3-Dimensional surface metrology products, precision positioning systems and custom-engineered solutions used in the semiconductor capital equipment, research, defense and industrial markets. Our Optical Systems segment designs, develops and manufactures high precision optical components and electro-optical systems used in the semiconductor capital equipment, defense, life sciences and research markets. The chief operating decision-maker uses this information to allocate resources.

The following table sets forth segment net revenues, gross profit and gross margin for the three months ended September 30, 2012 and 2011:

	Three Months Ended September 30,
	2012			2011
Metrology Solutions
Net revenues	$	25,878		$	29,842
Gross profit	$	14,335		$	17,370
Gross margin		55	%		58	%
Optical Systems
Net revenues	$	14,328		$	14,150
Gross profit	$	3,158		$	4,247
Gross margin		22	%		30	%
Total
Net revenues	$	40,206		$	43,992
Gross profit	$	17,493		$	21,617
Gross margin		44	%		49	%

Separate financial information by segment for total assets, capital expenditures and depreciation and amortization is not evaluated by our chief operating decision-maker. Substantially all of our operating expenses, assets and depreciation and amortization are U.S. based.

The following table sets forth revenues by geographic area:

	Three Months Ended September 30,
	2012		2011
Americas	$	18,863	$	24,293
Japan		6,331		6,786
China		7,538		6,080
Europe		4,822		4,271
Pacific Rim		2,652		2,562
Total	$	40,206	$	43,992

Revenues from two customers included in both segments accounted for 7% and 12% of the net revenues for the three months ended September 30, 2012 and for 11% and 10% of revenues for the three months ended September 30, 2011.