10-Q

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

FORM 10-Q

(Mark One)
x	QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the quarterly period ended                                                                              December 31, 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 filero	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.

18,513,181 shares of Common Stock, $.10 Par Value, at February 1, 2013

FORWARD LOOKING STATEMENTS

All statements other than statements of historical fact included in this Form 10-Q Quarterly Report regarding financial performance, condition and operations and the business strategy, plans, anticipated revenues, bookings, market acceptance, growth rates, market opportunities and objectives of management of the Company for future operations are forward-looking statements. Forward-looking statements provide management’s current expectations or plans for the future operating and financial performance of the Company based upon information currently available and assumptions currently believed to be valid. Forward-looking statements can be identified by the use of words such as “anticipate,” “believe,” “estimate,” “expect,” “intend,” “plan(s),” “strategy,” “project,” “should” and other words of similar meaning in connection with a discussion of current or future operating or financial performance. Actual results could differ materially from those contemplated by the forward-looking statements as a result of certain factors. Among the important factors that could cause actual events to differ materially from those in the forward-looking statements are fluctuations in capital spending of our customers; fluctuations in revenues to our major customers; manufacturing and supply chain risks; risks of booking cancellations, push-outs and de-bookings; dependence on timing and market acceptance of new product development; rapid technological and market change; risks in international operations; risks related to any reorganization of our business; risks related to changes in management personnel; dependence on proprietary technology and key personnel; length of the revenue cycle; environmental regulations; investment portfolio returns; fluctuations in our stock price; the risk that anticipated growth opportunities may be smaller than anticipated or may not be realized; and risks related to business acquisitions.

Any forward-looking statements included in this Quarterly Report speak only as of the date of this document. We undertake no obligation to publicly update or revise forward-looking statements to reflect events or circumstances after the date of this Form 10-Q except as required by law. Further information on potential factors that could affect our business is described in this Form 10-Q and in our reports on file with the Securities and Exchange Commission, including our Form 10-K for the fiscal year ended June 30, 2012, filed with the Securities and Exchange Commission on September 13, 2012.

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PART I - Financial Information

Item 1. Financial Statements

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
(UNAUDITED) (Amounts in thousands, except per share amounts)

	Three Months Ended December 31,						Six Months Ended December 31,
	2012			2011			2012			2011
Net revenue	$	34,635		$	40,040		$	74,841		$	84,032
Cost of goods sold		19,352			20,398			42,065			42,773
Gross profit		15,283			19,642			32,776			41,259
Selling, general and administrative expenses		8,568			8,107			17,089			17,570
Research, development and engineering expenses		4,502			4,087			9,083			8,149
Operating profit		2,213			7,448			6,604			15,540
Other income (expense)
Miscellaneous income (expense), net		(208	)		132			(172	)		(198	)
Total other income (expense)		(208	)		132			(172	)		(198	)
Income before income taxes, including noncontrolling interests		2,005			7,580			6,432			15,342
Income tax expense		(323	)		(823	)		(1,756	)		(1,609	)
Net income including noncontrolling interests		1,682			6,757			4,676			13,733
Less: Net income attributable to noncontrolling interests		103			579			709			1,086
Net income attributable to Zygo Corporation	$	1,579		$	6,178		$	3,967		$	12,647
Earnings per share attributable to Zygo Corporation
Basic earnings per share	$	0.09		$	0.34		$	0.22		$	0.71
Diluted earnings per share	$	0.08		$	0.33		$	0.21		$	0.68
Weighted average shares outstanding
Basic shares		18,455			17,930			18,398			17,865
Diluted shares		19,070			18,631			19,060			18,503

3

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME
(UNAUDITED) (Amounts in thousands)

	Three Months Ended December 31,						Six Months Ended December 31,
	2012			2011			2012		2011
Net income attributable to Zygo Corporation	$	1,579		$	6,178		$	3,967	$	12,647
Other comprehensive income (loss)
Foreign currency translation adjustment		(43	)		(272	)		365		(1,243	)
Comprehensive income		1,536			5,906			4,332		11,404
Less: Comprehensive income attributable to noncontrolling interests		38			(54	)		104		(261	)
Comprehensive income attributable to Zygo Corporation	$	1,498		$	5,960		$	4,228	$	11,665

See accompanying notes to condensed consolidated financial statements.

4

CONDENSED CONSOLIDATED BALANCE SHEETS
(UNAUDITED)
(Amounts in thousands, except share and per share amounts)

	December 31, 2012			June 30, 2012
Assets
Current assets:
Cash and cash equivalents	$	77,347		$	84,053
Receivables, net of allowance for doubtful accounts of $652 and $760, respectively		28,482			31,601
Inventories		29,928			27,760
Prepaid expenses, prepaid taxes and other current assets		6,062			2,851
Revenue recognized in excess of billings on uncompleted contracts		5,365			2,371
Deferred income taxes		11,337			8,004
Total current assets		158,521			156,640
Marketable securities		683			729
Property, plant and equipment, net		34,315			33,694
Deferred income taxes		13,766			13,760
Intangible assets, net		4,834			5,198
Total assets	$	212,119		$	210,021
Liabilities and Equity
Current liabilities:
Accounts payable	$	8,239		$	9,613
Progress payments and deferred revenue		5,813			5,482
Accrued salaries and wages		3,234			6,198
Other accrued expenses		6,385			7,234
Income taxes payable		386			416
Total current liabilities		24,057			28,943
Deferred income taxes		2,580			2,580
Other long-term liabilities		4,924			2,518
Total liabilities		31,561			34,041
Commitments and contingencies
Equity:
Common stock, $0.10 par value per share:
40,000,000 shares authorized;
20,798,084 shares issued (20,499,861 at June 30, 2012);
18,481,423 shares outstanding (18,239,941 at June 30, 2012)		2,080			2,050
Additional paid-in capital		178,369			176,305
Retained earnings		26,220			22,253
Accumulated other comprehensive income (loss):
Currency translation effects		75			(186	)
Treasury stock, at cost, 2,316,661 shares (2,259,920 at June 30, 2012)		(27,875	)		(26,797	)
Total shareholders’ equity - Zygo Corporation		178,869			173,625
Noncontrolling interests		1,689			2,355
Total equity		180,558			175,980
Total liabilities and equity	$	212,119		$	210,021

See accompanying notes to condensed consolidated financial statements.

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
(UNAUDITED)
(Amounts in thousands)

	Six Months Ended December 31,
	2012			2011
Cash provided by operating activities:
Net income including noncontrolling interests	$	4,676		$	13,733
Adjustments to reconcile net income to cash provided by operating activities from continuing operations:
Depreciation and amortization		2,783			2,921
Deferred income taxes		(2,105	)		—
Provision for doubtful accounts		(110	)		(280	)
Compensation cost related to share-based payment arrangements		2,756			2,318
Excess tax benefits from share-based payment arrangements		—			(298	)
Other		132			102
Changes in operating accounts:
Receivables		2,890			4,065
Inventories		(1,906	)		3,677
Prepaid expenses, prepaid taxes and other current assets		(3,012	)		113
Revenue recognized in excess of billings on uncompleted contracts		(2,994	)		—
Accounts payable, accrued expenses and taxes payable		(1,575	)		(1,926	)
Net cash provided by operating activities from continuing operations		1,535			24,425
Net cash used for operating activities from discontinued operations		—			(141	)
Cash used for investing activities:
Additions to property, plant and equipment		(3,510	)		(1,677	)
Purchase of marketable securities		—			(999	)
Additions to intangibles		(76	)		(89	)
Investments and acquisitions		(3,155	)		—
Proceeds from the sale and maturity of marketable securities		88			1,086
Net cash used for investing activities		(6,653	)		(1,679	)
Cash provided by (used for) financing activities:
Dividend payments to noncontrolling interest		(1,742	)		(746	)
Employee stock purchase		15			—
Excess tax benefits from share-based payment arrangements		—			298
Repurchase of restricted stock		(1,078	)		(301	)
Exercise of employee stock options		868			1,221
Net cash provided by (used for) financing activities		(1,937	)		472
Effect of exchange rate changes on cash and cash equivalents		349			(932	)
Net increase (decrease) in cash and cash equivalents		(6,706	)		22,145
Cash and cash equivalents, beginning of period		84,053			60,039
Cash and cash equivalents, end of period	$	77,347		$	82,184

Supplemental Cash Flow Information

Net cash paid for income taxes was $4,140 and $1,318 for the six months ended December 31, 2012 and 2011, respectively. Purchases of property, plant and equipment included in accounts payable was $132 and $76 for the six months ended December 31, 2012 and 2011, respectively.

See accompanying notes to condensed consolidated financial statements.

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NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED)
(Amounts in thousands, except share and per share amounts)

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 currencies; 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 and six months ended December 31, 2012 are not necessarily indicative of the results to be expected for the full fiscal year.

In management’s opinion, the accompanying balance sheets and related interim statements of income, comprehensive income, and cash flows 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.

Note 2: Earnings Per Share

For the three and six months ended December 31, 2012, outstanding stock options and restricted stock awards for 332,023 shares and 214,383 shares, respectively, (for the three and six months ended December 31, 2011, outstanding stock options and restricted stock awards for 310,966 shares and 362,490 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 December 31,				Six Months Ended December 31,
	2012		2011		2012		2011
Basic weighted average shares outstanding		18,455,136		17,930,226		18,398,228		17,864,990
Dilutive effect of stock options and and restricted shares		614,540		701,257		661,594		638,319
Diluted weighted average shares outstanding		19,069,676		18,631,483		19,059,822		18,503,309

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Note 3: Shareholders’ Equity

The following table sets forth shareholders’ equity and noncontrolling interest for the six months ended December 31, 2012 and 2011:

	Six Months Ended December 31,
	2012									2011
	Shareholders’ Equity			Non- Controlling			Total			Shareholders’ Equity			Non- Controlling			Total
	Zygo Corp.			Interest			Equity			Zygo Corp.			Interests			Equity
Equity, beginning of period	$	173,625		$	2,355		$	175,980		$	124,720		$	3,367		$	128,087
Net income		3,967			709			4,676			12,647			1,086			13,733
Foreign currency translation effect		261			104			365			(982	)		(261	)		(1,243	)
Total		4,228			813			5,041			11,665			825			12,490
Share based compensation		3,988			—			3,988			2,318			—			2,318
Repurchase of restricted stock		(1,078	)		—			(1,078	)		(301	)		—			(301	)
Employee Stock Purchase		15			—			15			—			—			—
Exercise of employee stock options and related tax effect		868			—			868			1,221			—			1,221
Dividends attributable to noncontrolling interests		—			(1,101	)		(1,101	)		—			(746	)		(746	)
Purchase of subsidiary shares from noncontrolling interest		(2,777	)		(378	)		(3,155	)		—			—			—
Equity, end of period	$	178,869		$	1,689		$	180,558		$	139,623		$	3,446		$	143,069

Note 4: Changes in Zygo Corporation Ownership Interest in Subsidiary

Zygo Corporation purchased the outstanding noncontrolling interest in our German subsidiary, ZygoLOT, for $3,155 in the first quarter of fiscal 2013. The following table sets forth the effects on equity of changes in our ownership interest of ZygoLOT.

	Six Months Ended December 31,
	2012		2011
Net income attributable to Zygo Corporation	$	3,967	$	12,647
Transfers to the noncontrolling interest
Decrease in Zygo Corporation paid in-capital for purchase of noncontrolling interest		2,749		—
Net transfers to noncontrolling interest		2,749		—
Change from net income attributable to Zygo Corporation shareholders and transfers to noncontrolling interest	$	1,218	$	12,647

8

Note 5: Marketable Securities

Marketable securities as of December 31, 2012 consisted of a mutual fund investment comprised primarily of corporate securities 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. We make 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 December 31, 2012 and 2011:

	Beginning Balance of Fiscal Year		Gross Unrealized Gains		Gross Unrealized Losses			Contri- butions		Redemp- tions			Ending Balance
December 31, 2012
Mutual Fund	$	729	$	42	$	—		$	—	$	(88	)	$	683
December 31, 2011
Mutual Fund	$	980	$	17	$	(134	)	$	—	$	(86	)	$	777

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 for similar products. 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 December 31, 2012 and June 30, 2012:

Assets Measured at Fair Value:

			Fair value measurements at December 31, 2012
	Total carrying value at December 31, 2012		Quoted prices in active markets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)
Money market funds	$	19,933	$	19,933	$	—	$	—
Trading securities		683		683		—		—
Foreign currency hedge		199		—		199		—
Total	$	20,815	$	20,616	$	199	$	—

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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	)	$	—

Note 7: Share-Based Payments

We recorded share-based compensation expense for the three months ended December 31, 2012 and 2011 of $1,526 and $1,089, respectively, with related tax benefits of $549 and $392, respectively. We also recorded share-based compensation expense for the six months ended December 31, 2012 and 2011 of $2,756 and $2,318, respectively, with related tax benefits of $992 and $835, 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 December 31, 2011 was $9.49. There were no stock option grants for the three months ended December 31, 2012. The weighted-average fair value of stock option grants for the six months ended December 31, 2012 and 2011 was $11.49 and $7.11, respectively. During the three months ended December 31, 2011, we issued stock options for an aggregate of 2,000 shares of common stock. For the three months ended December 31, 2012, no stock options were issued. During the six months ended December 31, 2012 and 2011, we issued stock options for an aggregate of 122,934 and 223,062 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 December 31,					Six Months Ended December 31,
	2012		2011			2012			2011
Term		n/a		6.6 Years			7.3 Years			6.6 Years
Volatility		n/a		59.5	%		59.2	%		59.5	%
Dividend yield		n/a		—			—			—
Risk-free interest rate		n/a		1.5	%		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 December 31, 2012 and 2011, an aggregate of 30,000 and 30,909 shares, respectively, of restricted stock units were issued at a weighted average stock price at date of grant of $14.52 and $16.91, respectively. During the six months ended December 31, 2012 and 2011, an aggregate of 162,901 and 146,412 shares, respectively, of restricted stock units were issued at a weighted average stock price at date of grant of $18.49 and $13.24, 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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Note 8: Receivables

The following table sets forth the components of accounts receivable at December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012
Trade	$	29,073		$	32,261
Other		61			100
		29,134			32,361
Allowance for doubtful accounts		(652	)		(760	)
	$	28,482		$	31,601

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 December 31, 2012 and June 30, 2012:

	December 31, 2012		June 30, 2012
Raw materials and manufactured parts	$	13,401	$	12,753
Work in process		13,145		12,031
Finished goods		3,382		2,976
	$	29,928	$	27,760

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 December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012			Estimated Useful Life (Years)
Land and improvements	$	4,030		$	4,030			—
Building and improvements		24,547			24,228			15-40
Machinery, equipment and office furniture		60,325			58,259			3-8
Leasehold improvements		1,074			964			1-5
Construction in progress		1,857			1,625			—
		91,833			89,106
Accumulated depreciation		(57,518	)		(55,412	)
	$	34,315		$	33,694

Depreciation expense was $1,169 and $1,259 for the three months ended December 31, 2012 and 2011, respectively, and $2,344 and $2,502 for the six months ended December 31, 2012 and 2011, respectively.

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Note 11: Warranty

A limited warranty is provided on our products for periods ranging from 3 to 12 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:

	Six Months Ended December 31,
	2012			2011
Beginning balance	$	1,188		$	1,333
Reductions for payments made		(467	)		(529	)
Changes in accruals related to pre-warranties		53			(103	)
Changes in accruals related to warranties made in the current period		287			552
Ending balance	$	1,061		$	1,253

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. As of December 31, 2012, all payments have been made 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 December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012
Patents	$	7,009		$	6,934
Customer relationships and technology		2,163			2,163
Covenant not-to-compete		851			851
		10,023			9,948
Accumulated amortization		(5,189	)		(4,750	)
Total	$	4,834		$	5,198

Amortization expense related to intangibles was $214 and $209 for the three months ended December 31, 2012 and 2011, respectively, compared with $439 and $419 for the six months ended December 31, 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 December 31, 2012, the estimated future amortization expense is as follows:

	Estimated Future Amortization Expense
Six months ending June 30, 2013	$	600
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		394
Fiscal year ending June 30, 2018		322
Thereafter		1,339
Total	$	4,834

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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 segments as Metrology Solutions and Optical Systems. The 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. The 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 and six months ended December 31, 2012 and 2011:

	Three Months Ended December 31,						Six Months Ended December 31,
	2012			2011			2012			2011
Metrology Solutions
Net revenues	$	21,416		$	25,479		$	47,294		$	55,321
Gross profit	$	11,595		$	15,057		$	25,928		$	32,440
Gross margin		54	%		59	%		55	%		59	%
Optical Systems
Net revenues	$	13,219		$	14,561		$	27,547		$	28,711
Gross profit	$	3,688		$	4,585		$	6,848		$	8,819
Gross margin		28	%		31	%		25	%		31	%
Total
Net revenues	$	34,635		$	40,040		$	74,841		$	84,032
Gross profit	$	15,283		$	19,642		$	32,776		$	41,259
Gross margin		44	%		49	%		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 December 31,				Six Months Ended December 31,
	2012		2011		2012		2011
Americas	$	19,755	$	22,170	$	38,618	$	46,461
Japan		5,336		5,692		11,667		12,479
China		3,498		3,823		11,036		9,903
Europe		4,397		5,834		9,219		10,105
Pacific Rim		1,649		2,521		4,301		5,084
Total	$	34,635	$	40,040	$	74,841	$	84,032

Revenues from two customers accounted for 14% and 11% of net revenues for the three months ended December 31, 2011. No customer accounted for over 10% of our revenues for the three months ended December 31, 2012. Revenues from one customer accounted for 10% of net revenues for the six months ended December 31, 2012. Revenues from two customers accounted for 12% and 11% of net revenues for the six months ended December 31, 2011. Revenues from these customers were included in both reporting segments.

13

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 $2,855 and $4,259 (8% and 11% of net revenues, respectively) for the three months ended December 31, 2012 and 2011, respectively. For the six months ended December 31, 2012 and 2011, revenues from Canon amounted to $5,668 and $9,053 (8% and 11% of net revenues, respectively). Selling prices of products sold to Canon are based, generally, on the terms customarily given to distributors. At December 31, 2012 and June 30, 2012, there were, in the aggregate, $1,193 and $1,604, respectively, of trade accounts receivable from Canon.

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 (expense).” 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 December 31, 2012, there were twelve currency contracts outstanding involving our Japanese operation with notional amounts aggregating $4,000. These foreign currency hedges are not designated as hedging instruments. For the three months ended December 31, 2012 and 2011, we recognized net unrealized gains of $244 and $39, respectively, from foreign currency forward contracts. For the six months ended December 31, 2012 and 2011, we recognized net unrealized gains of $201 and $70, 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 (expense)” on our condensed consolidated statements of operations.

The following table summarizes the fair value of derivative instruments as of December 31, 2012 and June 30, 2012:

Derivatives not designated as hedging instruments			Balance Sheet Location
			Prepaid expenses, prepaid
December 31, 2012	Number of foreign exchange contracts:	12	taxes and other current assets	$199
			Prepaid expenses, prepaid
June 30, 2012	Number of foreign exchange contracts:	9	taxes and other current assets	$14
			Other accrued expenses	$17

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Note 16: Income Taxes

	Three Months Ended December 31,										Six Months Ended December 31,
	2012					2011					2012					2011
	Amount		Tax Rate %			Amount		Tax Rate %			Amount		Tax Rate %			Amount		Tax Rate %
Income tax expense	$	323		16	%	$	823		11	%	$	1,756		27	%	$	1,609		10	%

Income tax expense for the three and six months ended December 31, 2012 related primarily to United States (“U.S.”) Federal and state income tax expense and foreign income tax expense and includes a tax benefit of $530 and $928 to correct an error in recording deferred tax asset balances as of June 30, 2012 relating primarily to fixed assets and foreign tax credits. Income tax expense for the three months ended December 31, 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 (“NOL”) 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 NOLs or credits available from those years are 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 and six months ended December 31, 2012, we recognized an additional liability of $217 and $407, respectively, 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.

Note 17: Commitments and Contingencies

On November 12, 2010, we completed a transaction with ASML US, Inc. (“ASML”) to purchase substantially all the assets of their Richmond, California operations. These assets were acquired for $12,475, of which $7,142 was in cash, and the balance was future consideration, with a net present value of $5,333 using a discount factor of 14%, based on the level of shipments to ASML over the subsequent three years beginning January 1, 2011. On the acquisition date, the future consideration was recorded as a liability, with $1,127 recorded as a current liability and $4,206 recorded as a long-term liability. The future consideration represented a supply agreement that was entered into with ASML that provided for a volume discount.

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

OVERVIEW

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. We conduct the majority of our manufacturing in a 153,500 square foot facility in Middlefield, Connecticut, a 55,300 square foot facility in Richmond, California, and a 22,560 square foot facility in Tucson, Arizona. In May 2012, we purchased a 110,020 square-foot facility in Tucson, Arizona, which will function as the manufacturing site for our Tucson operation when we complete our transition to the new site.

Bookings for the second quarter of fiscal 2013 were $42.8 million, a decrease of 13% compared with bookings of $48.8 million in the second quarter of fiscal 2012 and an increase of 15% compared with bookings of $37.3 million in the first quarter of fiscal 2013. Bookings for the Metrology Solutions segment were 62% of the total; Optical Systems segment bookings were 38%. Backlog was $73.2 million at December 31, 2012, compared with $69.7 million at December 31, 2011, and $65.1 million at September 30, 2012. Currently, 63% of the backlog is Optical System bookings which generally carry a lower gross margin than Metrology Solutions. If the mix of revenues changes to a greater proportion of Optics revenues, it is likely to adversely affect reported gross margin. The impact on gross margin will also depend on future bookings, particularly Metrology bookings with shorter shipping cycles.

Our effective tax rate increased as a result of the reversal of the valuation allowance on deferred tax assets in the fourth quarter of fiscal 2012. Previous years’ results benefitted from the offset effect of reversing valuation allowance against tax provision, essentially eliminating U.S. Federal income tax expense. Since the valuation allowance against deferred tax assets was eliminated at the end of fiscal 2012 due to improved operating performance and improved business outlook, current year results reflect tax expense at the full effective tax rate, modified by adjustment of prior period deferred tax asset balances as a component of the fiscal 2013 year tax provision.

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CRITICAL ACCOUNTING POLICIES, SIGNIFICANT JUDGMENTS AND ESTIMATES

The discussion and analysis of our financial condition and results of operations are based upon our condensed consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States of America. The preparation of these condensed consolidated financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenues, and expenses, and related disclosures at the date of our condensed consolidated financial statements. On an ongoing basis, management evaluates its estimates and judgments, including those related to bad debts, inventories, marketable securities, warranty obligations, income taxes, long-lived assets, share-based payments and accruals for health insurance. Management bases its estimates and judgments on historical experience and current market conditions and on various other factors that are believed to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions. As discussed in Item 7, “Management’s Discussion and Analysis of Financial Condition and Results of Operations” of the Company’s Annual Report on Form 10-K for the fiscal year ended June 30, 2012, management considers the Company’s policies on revenue recognition and allowance for doubtful accounts; inventory valuation; other-than-temporary impairment of marketable securities; share-based compensation; warranty costs; accounting for income taxes; valuation of long-lived assets; and accruals for health insurance to be critical accounting policies due to the estimates, assumptions and application of judgment involved in each.

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RESULTS OF OPERATIONS

Net Revenues by Segment

	Fiscal 2013					Fiscal 2012
(Amounts in millions)	Amount		Percentage of Total			Amount		Percentage of Total
Quarter ended December 31
Metrology Solutions	$	21.4		62	%	$	25.5		64	%
Optical Systems		13.2		38	%		14.5		36	%
Total	$	34.6		100	%	$	40.0		100	%
Six Months ended December 31
Metrology Solutions	$	47.3		63	%	$	55.3		66	%
Optical Systems		27.5		37	%		28.7		34	%
Total	$	74.8		100	%	$	84.0		100	%

Net revenues for the three months ended December 31, 2012 decreased $5.4 million, or 14%, compared with the prior year period, reflecting decreases in the Metrology Solutions segment revenues of 16% and in the Optical Systems segment of 9%. The decrease in the Metrology Solutions segment was primarily due to volume decreases of $3.0 million in instruments product lines related to microscopes and, to a lesser degree, large aperture systems and $0.8 million in certain product revenues attributable to soft demand in the semiconductor sector. The decrease in the Optical Systems segment was primarily due to volume decreases in optical components of $1.6 million and contract manufacturing of $0.3 million, partially offset by an increase in the extreme precision optics group of $0.5 million.

Net revenues for the six months ended December 31, 2012 decreased $9.2 million, or 11%, compared with the prior year period, reflecting decreases in the Metrology Solutions segment revenues of 15% and in the Optical Systems segment of 4%. The decrease in the Metrology Solutions segment of $8.0 million was primarily due to volume decreases in semiconductor related products of $5.6 million and instruments products of $3.1 million. The semiconductor market is still slow and has affected orders across several product lines. The Optical Systems segment declined $1.2 million year over year with increases in extreme precision optics of $3.7 million partially offsetting the declines in contract manufacturing and laser fusion optics.

Revenues from two customers accounted for 14% and 11% of net revenues for the three months ended December 31, 2011. No customer accounted for over 10% of revenues for the three months ended December 31, 2012. Revenues from one customer accounted for 10% of net revenues for the six months ended December 31, 2012. Revenues from two customers accounted for 12% and 11% of net revenues for the six months ended December 31, 2011. Revenues from these customers were included in both reporting segments.

Revenues denominated in U.S. dollars for the three months ended December 31, 2012 and 2011 were 76% and 79%, respectively, and 78% and 82% for the six months ended December 31, 2012 and 2011, respectively. The balance of revenue was denominated in Euro, Yen and Yuan. Revenues denominated in foreign currency are exposed to foreign exchange fluctuations from the time customers are invoiced in foreign currency until collection occurs. Significant changes in the values of foreign currencies relative to the value of the U.S. dollar, or in the general economic conditions in our export markets, could materially impact the revenues in these markets and our consolidated financial position and results of operations.

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Gross Margin by Segment

	Fiscal 2013					Fiscal 2012
(Amounts in millions)	Gross Profit		Gross Margin			Gross Profit		Gross Margin
Quarter ended December 31
Metrology Solutions	$	11.6		54	%	$	15.0		59	%
Optical Systems		3.7		28	%		4.6		32	%
Total	$	15.3		44	%	$	19.6		49	%
Six months ended December 31
Metrology Solutions	$	25.9		55	%	$	32.5		59	%
Optical Systems		6.9		25	%		8.8		31	%
Total	$	32.8		44	%	$	41.3		49	%

Gross margin for the three months ended December 31, 2012 was 44%, a decrease of five percentage points from the comparable prior year period. Within the Metrology Solutions segment, the decrease in gross margin for the three months ended December 31, 2012 compared with the prior year period was primarily due to a combination of overall lower volumes resulting in a decrease in labor and overhead absorption, lower margins on certain custom orders within the instruments product line and lower volumes in the semiconductor sector of products with traditionally more favorable gross margins. The gross margin of the Optical Systems segment for the three months ended December 31, 2012 decreased by four percentage points compared with the prior year period, primarily due to lower volumes, resulting in a decrease in labor and overhead absorption which increased other cost of sales and, to a lesser extent, lower than expected margins on certain custom orders.

Gross margin for the six months ended December 31, 2012 was 44%, a decrease of five percentage points from the comparable prior year period. Within the Metrology Solutions segment, the decrease in gross margin for the six months ended December 31, 2012 compared with the prior year period was primarily due to lower margins on certain custom orders within the instruments product line and the negative effect of lower volumes on labor and overhead absorption. The gross margin of the Optical Systems segment for the six months ended December 31, 2012 decreased by six percentage points compared with the prior year period, primarily due to a decrease in labor and overhead absorption.

Selling, General and Administrative Expenses (“SG&A”)

	Fiscal 2013					Fiscal 2012
(Amounts in millions)	Amount		Percentage of Net Revenues			Amount		Percentage of Net Revenues
Quarter ended December 31	$	8.6		25	%	$	8.1		20	%
Six months ended December 31	$	17.1		23	%	$	17.6		21	%

SG&A increased in the three months ended December 31, 2012 by $0.5 million from the comparable prior year period. The increase was primarily due to increased selling expense. For the six months ended December 31, 2012, SG&A decreased primarily due to lower employee incentive compensation partially offset by an increase in expenses related to increased headcount.

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Research, Development and Engineering Expenses (“RD&E”)

	Fiscal 2013					Fiscal 2012
(Amounts in millions)	Amount		Percentage of Net Revenues			Amount		Percentage of Net Revenues
Quarter ended December 31	$	4.5		13	%	$	4.1		10	%
Six months ended December 31	$	9.1		12	%	$	8.1		10	%

RD&E for the three months ended December 31, 2012 increased by $0.4 million compared with the prior year period primarily due to the increases in spending in our lithography stage metrology product line. RD&E expense for the six months ended December 31, 2012 increased by $1.0 million compared with the prior year period, primarily due to the increases in spending in our lithography stage metrology and extreme precision optics product lines.

Other Income (Expense)

	Fiscal 2013						Fiscal 2012
(Amounts in millions)	Amount			Percentage of Net Revenues			Amount			Percentage of Net Revenues
Quarter ended December 31	$	(0.2	)		1	%	$	0.1			0	%
Six months ended December 31	$	(0.2	)		0	%	$	(0.2	)		0	%

Other expense for the three and six months ended December 31, 2012 consisted primarily of imputed interest on a future contingent liability and foreign currency translation adjustments. Other income for the three months ended December 31, 2011 included a gain recorded due to a reduction in the anticipated future consideration expected to be paid by us related to a past acquisition.

Income Tax Expense

	Fiscal 2013					Fiscal 2012
(Amounts in millions)	Amount		Tax Rate %			Amount		Tax Rate %
Quarter ended December 31	$	0.3		16	%	$	0.8		11	%
Six months ended December 31	$	1.8		27	%	$	1.6		10	%

Income tax expense for the three months ended December 31, 2012 included income taxes in United States federal, state and foreign jurisdictions partially offset by a tax benefit of $0.5 million to correct an error in recording deferred tax asset balances as of June 30, 2012 relating to fixed assets recorded in an acquisition and foreign tax credits. Income tax expense for the three months ended December 31, 2011 included income taxes for state and foreign jurisdictions only. Income tax expense for the six months ended December 31, 2012 included a tax benefit of $0.9 million to correct an error in recording deferred tax asset balances as of June 30, 2012 related to fixed assets recorded in an acquisition and foreign tax credits. In the prior year for both the three and six month periods ended December 31, 2011, the valuation allowance recorded on substantially all net deferred tax assets, including those in the United States, effectively eliminated U.S. federal tax expense. The valuation allowance against deferred tax assets was eliminated at the end of fiscal 2012

20

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 $2.9 million and $4.3 million (8% and 11% of net revenues, respectively) for the three months ended December 31, 2012 and 2011, respectively. For the six months ended December 31, 2012 and 2011, revenues from Canon amounted to $5.7 million and $9.1 million (8% and 11% of net revenues, respectively). Selling prices of products sold to Canon are based, generally, on the terms customarily given to distributors. At December 31, 2012 and June 30, 2012, there were, in the aggregate, $1.2 million and $1.6 million, respectively, of trade accounts receivable from Canon.

LIQUIDITY AND CAPITAL RESOURCES

We assess our liquidity in terms of our ability to generate cash to fund our operating, investing and financing activities. Our principal source of liquidity is our cash reserves and operating cash flows. In addition to operating cash flows, other significant factors that affect our overall management of liquidity include: capital expenditures, customer credit requirements, investments in businesses and the availability of bank lines of credit.

At December 31, 2012, cash and cash equivalents were $77.3 million, a decrease of $6.8 million from $84.1 million at June 30, 2012. Cash in a money market account is invested primarily in U.S. government securities. We do not believe there is any risk to liquidity in the money market account, nor are there currently any limits on redemptions.

Cash provided by operating activities from continuing operations decreased period over period by $22.9 million to $1.5 million, due primarily to a decrease in net income of $9.1 million and a decrease in cash flows from fiscal 2012 to fiscal 2013 attributable to increases in inventories, unbilled costs on long-term contracts and prepaid taxes. The decrease in cash flows related to inventories is due to an increase in certain inventory lines for production in process on longer-term projects.

Cash used for investing activities increased $5.0 million to $6.7 million, due primarily to the buyout of the noncontrolling interest of ZygoLOT for $3.2 million (€2.5 million), and an increase in additions to property, plant and equipment of $1.8 million.

Cash used for financing activities increased $2.4 million to $1.9 million, due primarily to dividend payments to noncontrolling interests of $1.0 million and increases in the repurchase of restricted stock of $0.8 million.

We currently have no lines of credit. In the future, if the need for debt or credit lines arises, there is no assurance that we would be able to secure such financing. We believe we have sufficient cash flows from operations and cash reserves to maintain adequate amounts of liquidity and to meet our future liquidity requirements for at least the next twelve months.

21

OFF-BALANCE SHEET ARRANGEMENTS

We have not created, and are not party to, any special-purpose or off-balance sheet entities for the purpose of raising capital, incurring debt, or operating parts of our business that are not consolidated into our financial statements. We have not guaranteed any obligations of a third party.

Item 3. Quantitative and Qualitative Disclosures about Market Risk

There have been no material changes in our quantitative and qualitative market risk disclosures during the three months ended December 31, 2012. Please refer to Item 7a., “Quantitative and Qualitative Disclosures about Market Risk,” of our Annual Report on Form 10-K for the year ended June 30, 2012, filed with the Securities and Exchange Commission (the “2012 Annual Report”) for a discussion of our exposure to market risk.

Item 4. Controls and Procedures

The effectiveness of our or any system of disclosure controls and procedures is subject to certain limitations, including the exercise of judgment in designing, implementing, and evaluating the controls and procedures, the assumptions used in identifying the likelihood of future events, and the inability to eliminate misconduct completely. In designing, implementing, and evaluating the disclosure controls and procedures, our management recognized that any controls and procedures, no matter how well-designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and management necessarily was required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

We identified a material weakness as of June 30, 2012 related to inadequate design of processes, procedures and controls regarding our accounting for income taxes and, subsequently, concluded that our internal control over financial reporting was not effective at June 30, 2012. In the period since June 30, 2012, we have implemented, and are continuing to implement, additional controls in our financial reporting process, including adding control processes to aid in preparing the amounts related to certain tax assets and liabilities and the current and deferred income tax expense to ensure those amounts are recorded in accordance with accounting principles generally accepted in the United States of America, and have added external accounting resources to prepare and assist in the review of our accounting for income taxes. Certain controls designed and implemented to address the identified material weakness in the period-end financial reporting process have not had a sufficient period of time to operate for our management to conclude that they are operating effectively at December 31, 2012.

Our management, with the participation of our Chief Executive Officer and Principal Financial Officer, carried out an evaluation, as of the end of the period covered by this report (the quarter ended December 31, 2012), of the effectiveness of our disclosure controls and procedures (as such term is defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)), including controls and procedures implemented to address the material weakness described above. Based upon their evaluation and the lack of a sufficient period of time for the additional controls and processes to operate, the Chief Executive Officer and Principal Financial Officer concluded that, as of the end of such period, a material weakness still existed, and our disclosure controls and procedures were not effective in recording, processing, summarizing and reporting within the time periods specified in the Securities and Exchange Commission’s rules and forms information required to be disclosed by us in the reports that we file or submit under the Exchange Act and were not effective in ensuring that information required to be disclosed by us in the reports that we file or submit under the Exchange Act is accumulated and communicated to our management, including the Chief Executive Officer and Principal Financial Officer, as appropriate to allow timely decisions regarding required disclosure.

Except as described above, there were no changes in our internal control over financial reporting (as such term is defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) that occurred in the most recent fiscal quarter (the quarter ended December 31, 2012) that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

22

PART II - Other Information

Item 1A. Risk Factors

Part I, “Item 1A. Risk Factors” in our 2012 Annual Report includes a listing of risk factors that could materially affect our business, financial condition, or future results. There have been no material changes in risk factors from those set forth in our 2012 Annual Report; however, the risks described in our 2012 Annual Report are not the only risks facing the Company.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

The following table provides information about stock repurchases during the quarter ended December 31, 2012 under our authorized purchase plan in connection with the surrender of shares to cover taxes upon the vesting of restricted stock awards.

Period	Total number of shares purchased		Average price paid per share		Total number of shares purchased as part of publicly announced plans or programs (1)		Approximate dollar value of shares that may yet be purchased under the plans or programs (in millions)
October 1, 2012 - October 31, 2012		130	$	17.45		—	$	5.0
November 1, 2012 - November 30, 2012		—		n/a		—	$	5.0
December 1, 2012 - December 31, 2012		71	$	15.05		—	$	5.0

(1) In August 2007, our Board of Directors authorized the repurchase of up to $25.0 million of our outstanding common stock. During the three months ended December 31, 2012, there were no repurchases of common stock in the open market. The previous share repurchases under this program have been effected pursuant to plans in conformity with Rule 10b5-1 under the Securities Exchange Act of 1934. This rule allows public companies to adopt written, pre-arranged stock trading plans when they do not have material, non-public information in their possession. The adoption of this stock trading plan allows us to repurchase our shares during periods when we otherwise might be prevented from doing so under insider trading laws or because of self-imposed trading blackout periods.

23

Item 6. Exhibits
(a)	Exhibits:
	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

* 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.

24

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: February 11, 2013

25

EXHIBIT INDEX

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

* 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.

EX-31.1

EXHIBIT 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

I, Chris L. Koliopoulos, certify that:

1)	I have reviewed this quarterly report on Form 10-Q of Zygo Corporation;
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:	February 11, 2013
		/s/ Chris L. Koliopoulos
		Chris L. Koliopoulos
		President and Chief Executive Officer

EX-31.2

EXHIBIT 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

I, John P. Jordan, certify that:

1)	I have reviewed this quarterly report on Form 10-Q of Zygo Corporation;
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:	February 11, 2013
		/s/ John P. Jordan
		John P. Jordan
		Vice President, Chief Financial Officer and Treasurer

EX-32.1

EXHIBIT 32.1

CERTIFICATION PURSUANT TO 18 U.S.C. SECTION 1350, AS ADOPTED PURSUANT TO
SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

I, Chris L. Koliopoulos, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that the Quarterly Report of Zygo Corporation on Form 10-Q for the fiscal quarter ended December 31, 2012, as filed with the Securities and Exchange Commission (the “Report”), fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934 and that information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of Zygo Corporation.

A signed original of this written statement required by Section 906 has been provided to Zygo Corporation and will be retained by Zygo Corporation and furnished to the Securities and Exchange Commission or its staff upon request.

Dated: February 11, 2013

/s/ Chris L. Koliopoulos

Chris L. Koliopoulos

President and Chief Executive Officer

of Zygo Corporation

EX-32.2

EXHIBIT 32.2

CERTIFICATION PURSUANT TO 18 U.S.C. SECTION 1350, AS ADOPTED PURSUANT TO
SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

I, John P. Jordan, certify, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that the Quarterly Report of Zygo Corporation on Form 10-Q for the fiscal quarter ended December 31, 2012, as filed with the Securities and Exchange Commission (the “Report”), fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934 and that information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of Zygo Corporation.

A signed original of this written statement required by Section 906 has been provided to Zygo Corporation and will be retained by Zygo Corporation and furnished to the Securities and Exchange Commission or its staff upon request.

Dated: February 11, 2013

/s/ John P. Jordan

John P. Jordan

Vice President, Chief Financial Officer and Treasurer

of Zygo Corporation

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Income Taxes (Tables)

6 Months Ended

Dec. 31, 2012

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

Schedule of components of income tax expense benefit

	Three Months Ended December 31,										Six Months Ended December 31,
	2012					2011					2012					2011
	Amount		Tax Rate %			Amount		Tax Rate %			Amount		Tax Rate %			Amount		Tax Rate %
Income tax expense	$	323		16	%	$	823		11	%	$	1,756		27	%	$	1,609		10	%

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Warranty (Detail) - Schedule of product warranty liability (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Beginning balance	$ 1,188	$ 1,333
Reductions for payments made	(467)	(529)
Changes in accruals related to pre-warranties	53	(103)
Changes in accruals related to warranties made in the current period	287	552
Ending balance	$ 1,061	$ 1,253

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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	6 Months Ended
	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Term	6 years 219 days	7 years 109 days	6 years 219 days
Volatility	59.50%	59.20%	59.50%
Risk-free interest rate	1.50%	1.20%	1.50%

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Intangible Assets (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Amortization of Intangible Assets	$ 214	$ 209	$ 439	$ 419
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	Dec. 31, 2012	Jun. 30, 2012
Money market funds	$ 19,933	$ 19,931
Trading securities	683	729
Foreign currency hedge	199	(3)
Total	20,815	20,657
Fair Value, Inputs, Level 1 [Member]
Money market funds	19,933	19,931
Trading securities	683	729
Total	20,616	20,660
Fair Value, Inputs, Level 2 [Member]
Foreign currency hedge	199	(3)
Total	$ 199	$ (3)

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Inventories (Tables)

6 Months Ended

Dec. 31, 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 December 31, 2012 and June 30, 2012:

	December 31, 2012		June 30, 2012
Raw materials and manufactured parts	$	13,401	$	12,753
Work in process		13,145		12,031
Finished goods		3,382		2,976
	$	29,928	$	27,760

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Intangible Assets (Detail) - Estimated future amortization expense of intangible assets (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Jun. 30, 2012
Six months ending June 30, 2013	$ 600
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	394
Fiscal year ending June 30, 2018	322
Thereafter	1,339
Total	$ 4,834	$ 5,198

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Accounting Policies, by Policy (Policies)

6 Months Ended

Dec. 31, 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 currencies; 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 and six months ended December 31, 2012 are not necessarily indicative of the results to be expected for the full fiscal year.

In management’s opinion, the accompanying balance sheets and related interim statements of income, comprehensive income, and cash flows 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.

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Inventories (Detail) - Schedule of inventory current (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Jun. 30, 2012
Raw materials and manufactured parts	$ 13,401	$ 12,753
Work in process	13,145	12,031
Finished goods	3,382	2,976
	$ 29,928	$ 27,760

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Shareholders' Equity (Detail) - Shareholders' equity and noncontrolling interest (USD $) In Thousands, unless otherwise specified	3 Months Ended			6 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Equity, beginning of period		$ 173,625		$ 173,625
Net income	1,579		6,178	3,967	12,647
Foreign currency translation effect	(43)		(272)	365	(1,243)
Total	1,498		5,960	4,228	11,665
Share based compensation	1,526		1,089	2,756	2,318
Employee Stock Purchase				(15)
Exercise of employee stock options and related tax effect				868	1,221
Purchase of subsidiary shares from noncontrolling interest		3,155
Equity, end of period	178,869			178,869
Parent [Member]
Equity, beginning of period		173,625		173,625	124,720
Net income				3,967	12,647
Foreign currency translation effect				261	(982)
Total				4,228	11,665
Share based compensation				3,988	2,318
Repurchase of restricted stock				(1,078)	(301)
Employee Stock Purchase				15
Exercise of employee stock options and related tax effect				868	1,221
Purchase of subsidiary shares from noncontrolling interest				(2,777)
Equity, end of period	178,869		139,623	178,869	139,623
Noncontrolling Interest [Member]
Equity, beginning of period		2,355		2,355	3,367
Net income				709	1,086
Foreign currency translation effect				104	(261)
Total				813	825
Dividends attributable to noncontrolling interests				(1,101)	(746)
Purchase of subsidiary shares from noncontrolling interest				(378)
Equity, end of period	1,689		3,446	1,689	3,446
Total Equity [Member]
Equity, beginning of period		175,980		175,980	128,087
Net income				4,676	13,733
Foreign currency translation effect				365	(1,243)
Total				5,041	12,490
Share based compensation				3,988	2,318
Repurchase of restricted stock				(1,078)	(301)
Employee Stock Purchase				15
Exercise of employee stock options and related tax effect				868	1,221
Dividends attributable to noncontrolling interests				(1,101)	(746)
Purchase of subsidiary shares from noncontrolling interest				(3,155)
Equity, end of period	$ 180,558		$ 143,069	$ 180,558	$ 143,069

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Segment and Major Customer Information (Tables)

6 Months Ended

Dec. 31, 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 and six months ended December 31, 2012 and 2011:

	Three Months Ended December 31,						Six Months Ended December 31,
	2012			2011			2012			2011
Metrology Solutions
Net revenues	$	21,416		$	25,479		$	47,294		$	55,321
Gross profit	$	11,595		$	15,057		$	25,928		$	32,440
Gross margin		54	%		59	%		55	%		59	%
Optical Systems
Net revenues	$	13,219		$	14,561		$	27,547		$	28,711
Gross profit	$	3,688		$	4,585		$	6,848		$	8,819
Gross margin		28	%		31	%		25	%		31	%
Total
Net revenues	$	34,635		$	40,040		$	74,841		$	84,032
Gross profit	$	15,283		$	19,642		$	32,776		$	41,259
Gross margin		44	%		49	%		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 December 31,				Six Months Ended December 31,
	2012		2011		2012		2011
Americas	$	19,755	$	22,170	$	38,618	$	46,461
Japan		5,336		5,692		11,667		12,479
China		3,498		3,823		11,036		9,903
Europe		4,397		5,834		9,219		10,105
Pacific Rim		1,649		2,521		4,301		5,084
Total	$	34,635	$	40,040	$	74,841	$	84,032

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Property, Plant and Equipment (Detail) - Property plant and equipment (USD $) In Thousands, unless otherwise specified					6 Months Ended				6 Months Ended				6 Months Ended
	Dec. 31, 2012	Jun. 30, 2012	Dec. 31, 2012 Land Improvements [Member]	Jun. 30, 2012 Land Improvements [Member]	Dec. 31, 2012 Building and Building Improvements [Member] Minimum [Member]	Dec. 31, 2012 Building and Building Improvements [Member] Maximum [Member]	Dec. 31, 2012 Building and Building Improvements [Member]	Jun. 30, 2012 Building and Building Improvements [Member]	Dec. 31, 2012 Machinery Equipment And Office Furniture [Member] Minimum [Member]	Dec. 31, 2012 Machinery Equipment And Office Furniture [Member] Maximum [Member]	Dec. 31, 2012 Machinery Equipment And Office Furniture [Member]	Jun. 30, 2012 Machinery Equipment And Office Furniture [Member]	Dec. 31, 2012 Leasehold Improvements [Member] Minimum [Member]	Dec. 31, 2012 Leasehold Improvements [Member] Maximum [Member]	Dec. 31, 2012 Leasehold Improvements [Member]	Jun. 30, 2012 Leasehold Improvements [Member]	Dec. 31, 2012 Construction in Progress [Member]	Jun. 30, 2012 Construction in Progress [Member]
Property, Plant and Equipment, Gross	$ 91,833	$ 89,106	$ 4,030	$ 4,030			$ 24,547	$ 24,228			$ 60,325	$ 58,259			$ 1,074	$ 964	$ 1,857	$ 1,625
Property, Plant and Equipment, Useful Life					15 years	40 years			3 years	8 years			1 year	5 years
Accumulated depreciation	(57,518)	(55,412)
	$ 34,315	$ 33,694

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Transactions with Shareholder (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011	Jun. 30, 2012
Revenue, Net	$ 34,635	$ 40,040	$ 74,841	$ 84,032
Accounts Receivable, Net, Current	28,482		28,482		31,601
Trade Accounts Receivable [Member] | Canon Inc [Member]
Accounts Receivable, Net, Current	1,193		1,193		1,604
Japan And Subsidiary Of Canon Inc [Member]
Revenue, Net	$ 2,855	$ 4,259	$ 5,668	$ 9,053
Percentage Of Net Revenues	8.00%	11.00%	8.00%	11.00%

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Share-Based Payments (Detail) (USD $) In Thousands, except Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Share-based Compensation (in Dollars)	$ 1,526	$ 1,089	$ 2,756	$ 2,318
Employee Service Share-based Compensation, Tax Benefit from Compensation Expense (in Dollars)	$ 549	$ 392	$ 992	$ 835
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Weighted Average Grant Date Fair Value (in Dollars per share)		$ 9.49	$ 11.49	$ 7.11
Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Net of Forfeitures	0	2,000	122,934	223,062
Restricted Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	30,000	30,909	162,901	146,412
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)	$ 14.52	$ 16.91	$ 18.49	$ 13.24
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

6 Months Ended

Dec. 31, 2012

Earnings Per Share [Text Block]

Note 2: Earnings Per Share

For the three and six months ended December 31, 2012, outstanding stock options and restricted stock awards for 332,023 shares and 214,383 shares, respectively, (for the three and six months ended December 31, 2011, outstanding stock options and restricted stock awards for 310,966 shares and 362,490 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 December 31,				Six Months Ended December 31,
	2012		2011		2012		2011
Basic weighted average shares outstanding		18,455,136		17,930,226		18,398,228		17,864,990
Dilutive effect of stock options and and restricted shares		614,540		701,257		661,594		638,319
Diluted weighted average shares outstanding		19,069,676		18,631,483		19,059,822		18,503,309

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Derivatives and Hedging Activities (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Notional Amount of Foreign Currency Derivative Instruments Not Designated as Hedging Instruments	$ 4,000		$ 4,000
Foreign Currency Transaction Gain (Loss), Unrealized	$ 244	$ 39	$ 201	$ 70

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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)

6 Months Ended

Dec. 31, 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 December 31, 2012 and 2011:

	Beginning Balance of Fiscal Year		Gross Unrealized Gains		Gross Unrealized Losses			Contri- butions		Redemp- tions			Ending Balance
December 31, 2012
Mutual Fund	$	729	$	42	$	—		$	—	$	(88	)	$	683
December 31, 2011
Mutual Fund	$	980	$	17	$	(134	)	$	—	$	(86	)	$	777

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

6 Months Ended

Dec. 31, 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.

	Six Months Ended December 31,
	2012		2011
Net income attributable to Zygo Corporation	$	3,967	$	12,647
Transfers to the noncontrolling interest
Decrease in Zygo Corporation paid in-capital for purchase of noncontrolling interest		2,749		—
Net transfers to noncontrolling interest		2,749		—
Change from net income attributable to Zygo Corporation shareholders and transfers to noncontrolling interest	$	1,218	$	12,647

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Intangible Assets (Detail) - Schedule of finite lived intangible assets (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Jun. 30, 2012
Intangible assets, gross	$ 10,023	$ 9,948
Accumulated amortization	(5,189)	(4,750)
Total	4,834	5,198
Patents And Trademarks [Member]
Intangible assets, gross	7,009	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		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Net income attributable to Zygo Corporation	$ 1,579	$ 6,178	$ 3,967	$ 12,647
Transfers to the noncontrolling interest
Decrease in Zygo Corporation paid in-capital for purchase of noncontrolling interest			2,749
Net transfers to noncontrolling interest			2,749
Change from net income attributable to Zygo Corporation shareholders and transfers to noncontrolling interest			$ 1,218	$ 12,647

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Fair Value Measurements (Tables)

6 Months Ended

Dec. 31, 2012

The following tables provide the assets and liabilities carried at fair value measured on a recurring basis as of December 31, 2012 and June 30, 2012:

			Fair value measurements at December 31, 2012
	Total carrying value at December 31, 2012		Quoted prices in active markets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)
Money market funds	$	19,933	$	19,933	$	—	$	—
Trading securities		683		683		—		—
Foreign currency hedge		199		—		199		—
Total	$	20,815	$	20,616	$	199	$	—

				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)

6 Months Ended

Dec. 31, 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 December 31,					Six Months Ended December 31,
	2012		2011			2012			2011
Term		n/a		6.6 Years			7.3 Years			6.6 Years
Volatility		n/a		59.5	%		59.2	%		59.5	%
Dividend yield		n/a		—			—			—
Risk-free interest rate		n/a		1.5	%		1.2	%		1.5	%

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Accounting Policies

6 Months Ended

Dec. 31, 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 currencies; 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 and six months ended December 31, 2012 are not necessarily indicative of the results to be expected for the full fiscal year.

In management’s opinion, the accompanying balance sheets and related interim statements of income, comprehensive income, and cash flows 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.

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Receivables (Tables)

6 Months Ended

Dec. 31, 2012

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

The following table sets forth the components of accounts receivable at December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012
Trade	$	29,073		$	32,261
Other		61			100
		29,134			32,361
Allowance for doubtful accounts		(652	)		(760	)
	$	28,482		$	31,601

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Earnings Per Share (Detail)	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	332,023	310,966	214,383	362,490

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Warranty (Detail)	3 Months Ended
	Dec. 31, 2012
Standard Product Warranty Description	A limited warranty is provided on our products for periods ranging from 3 to 12 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		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Net revenue	$ 34,635	$ 40,040	$ 74,841	$ 84,032
Cost of goods sold	19,352	20,398	42,065	42,773
Gross profit	15,283	19,642	32,776	41,259
Selling, general and administrative expenses	8,568	8,107	17,089	17,570
Research, development and engineering expenses	4,502	4,087	9,083	8,149
Operating profit	2,213	7,448	6,604	15,540
Other income (expense)
Miscellaneous income (expense), net	(208)	132	(172)	(198)
Total other income (expense)	(208)	132	(172)	(198)
Income before income taxes, including noncontrolling interests	2,005	7,580	6,432	15,342
Income tax expense	(323)	(823)	(1,756)	(1,609)
Net income including noncontrolling interests	1,682	6,757	4,676	13,733
Less: Net income attributable to noncontrolling interests	103	579	709	1,086
Net income attributable to Zygo Corporation	$ 1,579	$ 6,178	$ 3,967	$ 12,647
Earnings per share attributable to Zygo Corporation
Basic earnings per share (in Dollars per share)	$ 0.09	$ 0.34	$ 0.22	$ 0.71
Diluted earnings per share (in Dollars per share)	$ 0.08	$ 0.33	$ 0.21	$ 0.68
Weighted average shares outstanding
Basic shares (in Shares)	18,455,136	17,930,226	18,398,228	17,864,990
Diluted shares (in Shares)	19,069,676	18,631,483	19,059,822	18,503,309

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Marketable Securities (Detail) - Schedule of trading securities (Mutual Fund [Member], USD $) In Thousands, unless otherwise specified	6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Mutual Fund [Member]
Beginning Balance of Fiscal Year	$ 729	$ 980
Gross Unrealized Gains	42	17
Gross Unrealized Losses		(134)
Redemptions	(88)	(86)
Ending Balance	$ 683	$ 777

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Cash provided by operating activities:
Net income including noncontrolling interests	$ 4,676	$ 13,733
Adjustments to reconcile net income to cash provided by operating activities from continuing operations:
Depreciation and amortization	2,783	2,921
Deferred income taxes	(2,105)
Provision for doubtful accounts	(110)	(280)
Compensation cost related to share-based payment arrangements	2,756	2,318
Excess tax benefits from share-based payment arrangements		(298)
Other	132	102
Changes in operating accounts:
Receivables	2,890	4,065
Inventories	(1,906)	3,677
Prepaid expenses, prepaid taxes and other current assets	(3,012)	113
Revenue recognized in excess of billings on uncompleted contracts	(2,994)
Accounts payable, accrued expenses and taxes payable	(1,575)	(1,926)
Net cash provided by operating activities from continuing operations	1,535	24,425
Net cash used for operating activities from discontinued operations		(141)
Cash used for investing activities:
Additions to property, plant and equipment	(3,510)	(1,677)
Purchase of marketable securities		(999)
Additions to intangibles	(76)	(89)
Investments and acquisitions	(3,155)
Proceeds from the sale and maturity of marketable securities	88	1,086
Net cash used for investing activities	(6,653)	(1,679)
Cash provided by (used for) financing activities:
Dividend payments to noncontrolling interest	(1,742)	(746)
Employee stock purchase	15
Excess tax benefits from share-based payment arrangements		298
Repurchase of restricted stock	(1,078)	(301)
Exercise of employee stock options	868	1,221
Net cash provided by (used for) financing activities	(1,937)	472
Effect of exchange rate changes on cash and cash equivalents	349	(932)
Net increase (decrease) in cash and cash equivalents	(6,706)	22,145
Cash and cash equivalents, beginning of period	84,053	60,039
Cash and cash equivalents, end of period	$ 77,347	$ 82,184

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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		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Net revenues	$ 34,635	$ 40,040	$ 74,841	$ 84,032
Gross profit	15,283	19,642	32,776	41,259
Gross margin	44.00%	49.00%	44.00%	49.00%
Metrology Solutions [Member]
Net revenues	21,416	25,479	47,294	55,321
Gross profit	11,595	15,057	25,928	32,440
Gross margin	54.00%	59.00%	55.00%	59.00%
Optical Systems [Member]
Net revenues	13,219	14,561	27,547	28,711
Gross profit	$ 3,688	$ 4,585	$ 6,848	$ 8,819
Gross margin	28.00%	31.00%	25.00%	31.00%

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Warranty (Tables)

6 Months Ended

Dec. 31, 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:

	Six Months Ended December 31,
	2012			2011
Beginning balance	$	1,188		$	1,333
Reductions for payments made		(467	)		(529	)
Changes in accruals related to pre-warranties		53			(103	)
Changes in accruals related to warranties made in the current period		287			552
Ending balance	$	1,061		$	1,253

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Income Taxes (Detail) - Schedule of components of income tax expense benefit (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Income tax expense (in Dollars)	$ 323	$ 823	$ 1,756	$ 1,609
Income tax expense	16.00%	11.00%	27.00%	10.00%

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Derivatives and Hedging Activities

6 Months Ended

Dec. 31, 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 (expense).” 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 December 31, 2012, there were twelve currency contracts outstanding involving our Japanese operation with notional amounts aggregating $4,000. These foreign currency hedges are not designated as hedging instruments. For the three months ended December 31, 2012 and 2011, we recognized net unrealized gains of $244 and $39, respectively, from foreign currency forward contracts. For the six months ended December 31, 2012 and 2011, we recognized net unrealized gains of $201 and $70, 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 (expense)” on our condensed consolidated statements of operations.

The following table summarizes the fair value of derivative instruments as of December 31, 2012 and June 30, 2012:

Derivatives not designated as hedging instruments			Balance Sheet Location
December 31, 2012	Number of foreign exchange contracts:	12	Prepaid expenses, prepaid taxes and other current assets	$199
June 30, 2012	Number of foreign exchange contracts:	9	Prepaid expenses, prepaid taxes and other current assets	$14
			Other accrued expenses	$17

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Intangible Assets (Tables)

6 Months Ended

Dec. 31, 2012

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

The following table sets forth the components of intangible assets, as of December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012
Patents	$	7,009		$	6,934
Customer relationships and technology		2,163			2,163
Covenant not-to-compete		851			851
		10,023			9,948
Accumulated amortization		(5,189	)		(4,750	)
Total	$	4,834		$	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 December 31, 2012, the estimated future amortization expense is as follows:

	Estimated Future Amortization Expense
Six months ending June 30, 2013	$	600
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		394
Fiscal year ending June 30, 2018		322
Thereafter		1,339
Total	$	4,834

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Commitments and Contingencies

6 Months Ended

Dec. 31, 2012

Commitments and Contingencies Disclosure [Text Block]

Note 17: Commitments and Contingencies

On November 12, 2010, we completed a transaction with ASML US, Inc. (“ASML”) to purchase substantially all the assets of their Richmond, California operations. These assets were acquired for $12,475, of which $7,142 was in cash, and the balance was future consideration, with a net present value of $5,333 using a discount factor of 14%, based on the level of shipments to ASML over the subsequent three years beginning January 1, 2011. On the acquisition date, the future consideration was recorded as a liability, with $1,127 recorded as a current liability and $4,206 recorded as a long-term liability. The future consideration represented a supply agreement that was entered into with ASML that provided for a volume discount.

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	6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Net cash paid for income taxes	$ 4,140	$ 1,318
Purchases of property, plant and equipment included in accounts payable	$ 132	$ 76

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CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Net income attributable to Zygo Corporation	$ 1,579	$ 6,178	$ 3,967	$ 12,647
Other comprehensive income (loss)
Foreign currency translation adjustment	(43)	(272)	365	(1,243)
Comprehensive income	1,536	5,906	4,332	11,404
Less: Comprehensive income attributable to noncontrolling interests	38	(54)	104	(261)
Comprehensive income attributable to Zygo Corporation	$ 1,498	$ 5,960	$ 4,228	$ 11,665

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Property, Plant and Equipment

6 Months Ended

Dec. 31, 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 December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012			Estimated Useful Life (Years)
							Min	Max
Land and improvements	$	4,030		$	4,030
Building and improvements		24,547			24,228		15	40
Machinery, equipment and office furniture		60,325			58,259		3	8
Leasehold improvements		1,074			964		1	5
Construction in progress		1,857			1,625
		91,833			89,106
Accumulated depreciation		(57,518	)		(55,412	)
	$	34,315		$	33,694

Depreciation expense was $1,169 and $1,259 for the three months ended December 31, 2012 and 2011, respectively, and $2,344 and $2,502 for the six months ended December 31, 2012 and 2011, respectively.

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Document And Entity Information	6 Months Ended
	Dec. 31, 2012	Feb. 01, 2013
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		18,513,181
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	Dec. 31, 2012
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q2

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Warranty

6 Months Ended

Dec. 31, 2012

Product Warranty Disclosure [Text Block]

Note 11: Warranty

A limited warranty is provided on our products for periods ranging from 3 to 12 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:

	Six Months Ended December 31,
	2012			2011
Beginning balance	$	1,188		$	1,333
Reductions for payments made		(467	)		(529	)
Changes in accruals related to pre-warranties		53			(103	)
Changes in accruals related to warranties made in the current period		287			552
Ending balance	$	1,061		$	1,253

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CONDENSED CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Jun. 30, 2012
Current assets:
Cash and cash equivalents	$ 77,347	$ 84,053
Receivables, net of allowance for doubtful accounts of $652 and $760, respectively	28,482	31,601
Inventories	29,928	27,760
Prepaid expenses, prepaid taxes and other current assets	6,062	2,851
Revenue recognized in excess of billings on uncompleted contracts	5,365	2,371
Deferred income taxes	11,337	8,004
Total current assets	158,521	156,640
Marketable securities	683	729
Property, plant and equipment, net	34,315	33,694
Deferred income taxes	13,766	13,760
Intangible assets, net	4,834	5,198
Total assets	212,119	210,021
Current liabilities:
Accounts payable	8,239	9,613
Progress payments and deferred revenue	5,813	5,482
Accrued salaries and wages	3,234	6,198
Other accrued expenses	6,385	7,234
Income taxes payable	386	416
Total current liabilities	24,057	28,943
Deferred income taxes	2,580	2,580
Other long-term liabilities	4,924	2,518
Total liabilities	31,561	34,041
Commitments and contingencies
Equity:
Common stock, $0.10 par value per share: 40,000,000 shares authorized; 20,798,084 shares issued (20,499,861 at June 30, 2012); 18,481,423 shares outstanding (18,239,941 at June 30, 2012)	2,080	2,050
Additional paid-in capital	178,369	176,305
Retained earnings	26,220	22,253
Accumulated other comprehensive income (loss):
Currency translation effects	75	(186)
Treasury stock, at cost, 2,316,661 shares (2,259,920 at June 30, 2012)	(27,875)	(26,797)
Total shareholders’ equity - Zygo Corporation	178,869	173,625
Noncontrolling interests	1,689	2,355
Total equity	180,558	175,980
Total liabilities and equity	$ 212,119	$ 210,021

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Marketable Securities

6 Months Ended

Dec. 31, 2012

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

Note 5: Marketable Securities

Marketable securities as of December 31, 2012 consisted of a mutual fund investment comprised primarily of corporate securities 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. We make 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 December 31, 2012 and 2011:

	Beginning Balance of Fiscal Year		Gross Unrealized Gains		Gross Unrealized Losses			Contri- butions		Redemp- tions			Ending Balance
December 31, 2012
Mutual Fund	$	729	$	42	$	—		$	—	$	(88	)	$	683
December 31, 2011
Mutual Fund	$	980	$	17	$	(134	)	$	—	$	(86	)	$	777

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Changes in Zygo Corporation's Ownership Interest in Subsidiary

6 Months Ended

Dec. 31, 2012

Changes In Ownership Interest In Subsidiary [Text Block]

Note 4: Changes in Zygo Corporation Ownership Interest in Subsidiary

Zygo Corporation purchased the outstanding noncontrolling interest in our German subsidiary, ZygoLOT, for $3,155 in the first quarter of fiscal 2013. The following table sets forth the effects on equity of changes in our ownership interest of ZygoLOT.

	Six Months Ended December 31,
	2012		2011
Net income attributable to Zygo Corporation	$	3,967	$	12,647
Transfers to the noncontrolling interest
Decrease in Zygo Corporation paid in-capital for purchase of noncontrolling interest		2,749		—
Net transfers to noncontrolling interest		2,749		—
Change from net income attributable to Zygo Corporation shareholders and transfers to noncontrolling interest	$	1,218	$	12,647

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Income Taxes

6 Months Ended

Dec. 31, 2012

Income Tax Disclosure [Text Block]

Note 16: Income Taxes

	Three Months Ended December 31,										Six Months Ended December 31,
	2012					2011					2012					2011
	Amount		Tax Rate %			Amount		Tax Rate %			Amount		Tax Rate %			Amount		Tax Rate %
Income tax expense	$	323		16	%	$	823		11	%	$	1,756		27	%	$	1,609		10	%

Income tax expense for the three and six months ended December 31, 2012 related primarily to United States (“U.S.”) Federal and state income tax expense and foreign income tax expense and includes a tax benefit of $530 and $928 to correct an error in recording deferred tax asset balances as of June 30, 2012 relating primarily to fixed assets and foreign tax credits. Income tax expense for the three months ended December 31, 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 (“NOL”) 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 NOLs or credits available from those years are 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 and six months ended December 31, 2012, we recognized an additional liability of $217 and $407, respectively, 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

6 Months Ended

Dec. 31, 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. As of December 31, 2012, all payments have been made 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 December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012
Patents	$	7,009		$	6,934
Customer relationships and technology		2,163			2,163
Covenant not-to-compete		851			851
		10,023			9,948
Accumulated amortization		(5,189	)		(4,750	)
Total	$	4,834		$	5,198

Amortization expense related to intangibles was $214 and $209 for the three months ended December 31, 2012 and 2011, respectively, compared with $439 and $419 for the six months ended December 31, 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 December 31, 2012, the estimated future amortization expense is as follows:

	Estimated Future Amortization Expense
Six months ending June 30, 2013	$	600
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		394
Fiscal year ending June 30, 2018		322
Thereafter		1,339
Total	$	4,834

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Receivables

6 Months Ended

Dec. 31, 2012

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

Note 8: Receivables

The following table sets forth the components of accounts receivable at December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012
Trade	$	29,073		$	32,261
Other		61			100
		29,134			32,361
Allowance for doubtful accounts		(652	)		(760	)
	$	28,482		$	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		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Sales Revenue Net	$ 34,635	$ 40,040	$ 74,841	$ 84,032
Americas [Member]
Sales Revenue Net	19,755	22,170	38,618	46,461
Japan [Member]
Sales Revenue Net	5,336	5,692	11,667	12,479
China [Member]
Sales Revenue Net	3,498	3,823	11,036	9,903
Europe [Member]
Sales Revenue Net	4,397	5,834	9,219	10,105
Pacific Rim [Member]
Sales Revenue Net	$ 1,649	$ 2,521	$ 4,301	$ 5,084

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Fair Value Measurements

6 Months Ended

Dec. 31, 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 for similar products. 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 December 31, 2012 and June 30, 2012:

Assets Measured at Fair Value:

			Fair value measurements at December 31, 2012
	Total carrying value at December 31, 2012		Quoted prices in active markets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)
Money market funds	$	19,933	$	19,933	$	—	$	—
Trading securities		683		683		—		—
Foreign currency hedge		199		—		199		—
Total	$	20,815	$	20,616	$	199	$	—

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

6 Months Ended

Dec. 31, 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 December 31, 2012 and 2011 of $1,526 and $1,089, respectively, with related tax benefits of $549 and $392, respectively. We also recorded share-based compensation expense for the six months ended December 31, 2012 and 2011 of $2,756 and $2,318, respectively, with related tax benefits of $992 and $835, 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 December 31, 2011 was $9.49. There were no stock option grants for the three months ended December 31, 2012. The weighted-average fair value of stock option grants for the six months ended December 31, 2012 and 2011 was $11.49 and $7.11, respectively. During the three months ended December 31, 2011, we issued stock options for an aggregate of 2,000 shares of common stock. For the three months ended December 31, 2012, no stock options were issued. During the six months ended December 31, 2012 and 2011, we issued stock options for an aggregate of 122,934 and 223,062 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 December 31,					Six Months Ended December 31,
	2012		2011			2012			2011
Term		n/a		6.6 Years			7.3 Years			6.6 Years
Volatility		n/a		59.5	%		59.2	%		59.5	%
Dividend yield		n/a		—			—			—
Risk-free interest rate		n/a		1.5	%		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 December 31, 2012 and 2011, an aggregate of 30,000 and 30,909 shares, respectively, of restricted stock units were issued at a weighted average stock price at date of grant of $14.52 and $16.91, respectively. During the six months ended December 31, 2012 and 2011, an aggregate of 162,901 and 146,412 shares, respectively, of restricted stock units were issued at a weighted average stock price at date of grant of $18.49 and $13.24, 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

6 Months Ended

Dec. 31, 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 December 31, 2012 and June 30, 2012:

	December 31, 2012		June 30, 2012
Raw materials and manufactured parts	$	13,401	$	12,753
Work in process		13,145		12,031
Finished goods		3,382		2,976
	$	29,928	$	27,760

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Income Taxes (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended	6 Months Ended
	Dec. 31, 2012	Dec. 31, 2012
Tax Benefit To Correct Error In Deferred Tax Asset	$ 530	$ 928
Additional Liability for Changes In Tax Positions	$ 217	$ 407

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Commitments and Contingencies (Detail) (USD $) In Thousands, unless otherwise specified	Nov. 12, 2010
Business Acquisition, Cost of Acquired Entity, Purchase Price	$ 12,475
Business Acquisition, Cost of Acquired Entity, Cash Paid	7,142
Business Acquisition, Cost of Acquired Entity, Liabilities Incurred	5,333
Business Acquisition, Cost Of Acquired Entity, Liabilities Incurred, Discount Factor	14.00%
Business Acquisition, Cost of Acquired Entity, Current Liabilities Incurred	1,127
Business Acquisition, Cost of Acquired Entity, Long-term Liabilities Incurred	$ 4,206

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Derivatives and Hedging Activities (Detail) - Schedule of foreign exchange contracts statement of financial position (USD $) In Thousands, unless otherwise specified	6 Months Ended	12 Months Ended
	Dec. 31, 2012	Jun. 30, 2012
Prepaid Expense And Other [Member]
Number of foreign exchange contracts	12	9
Balance Sheet Location	Prepaid expenses, prepaid taxes and other current assets	Prepaid expenses, prepaid taxes and other current assets
Fair value of derivative instruments	$ 199	$ 14
Other Accrued Liabilities [Member]
Balance Sheet Location		Other accrued expenses
Fair value of derivative instruments		$ 17

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Property, Plant and Equipment (Tables)

6 Months Ended

Dec. 31, 2012

Property, Plant and Equipment [Table Text Block]

The following table sets forth the components of property, plant and equipment at December 31, 2012 and June 30, 2012:

	December 31, 2012			June 30, 2012			Estimated Useful Life (Years)
							Min	Max
Land and improvements	$	4,030		$	4,030
Building and improvements		24,547			24,228		15	40
Machinery, equipment and office furniture		60,325			58,259		3	8
Leasehold improvements		1,074			964		1	5
Construction in progress		1,857			1,625
		91,833			89,106
Accumulated depreciation		(57,518	)		(55,412	)
	$	34,315		$	33,694

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Property, Plant and Equipment (Detail) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Depreciation	$ 1,169	$ 1,259	$ 2,344	$ 2,502

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Transactions with Shareholder

6 Months Ended

Dec. 31, 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 $2,855 and $4,259 (8% and 11% of net revenues, respectively) for the three months ended December 31, 2012 and 2011, respectively. For the six months ended December 31, 2012 and 2011, revenues from Canon amounted to $5,668 and $9,053 (8% and 11% of net revenues, respectively). Selling prices of products sold to Canon are based, generally, on the terms customarily given to distributors. At December 31, 2012 and June 30, 2012, there were, in the aggregate, $1,193 and $1,604, respectively, of trade accounts receivable from Canon.

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Earnings Per Share (Tables)

6 Months Ended

Dec. 31, 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 December 31,				Six Months Ended December 31,
	2012		2011		2012		2011
Basic weighted average shares outstanding		18,455,136		17,930,226		18,398,228		17,864,990
Dilutive effect of stock options and and restricted shares		614,540		701,257		661,594		638,319
Diluted weighted average shares outstanding		19,069,676		18,631,483		19,059,822		18,503,309

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Receivables (Detail) - Schedule of accounts notes receivable (USD $) In Thousands, unless otherwise specified	Dec. 31, 2012	Jun. 30, 2012
Receivables	$ 29,134	$ 32,361
Allowance for doubtful accounts	(652)	(760)
	28,482	31,601
Trade Accounts Receivable [Member]
Receivables	29,073	32,261
Other Receiveable [Member]
Receivables	$ 61	$ 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		6 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2012	Dec. 31, 2011
Basic weighted average shares outstanding	18,455,136	17,930,226	18,398,228	17,864,990
Dilutive effect of stock options and and restricted shares	614,540	701,257	661,594	638,319
Diluted weighted average shares outstanding	19,069,676	18,631,483	19,059,822	18,503,309

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CONDENSED CONSOLIDATED BALANCE SHEETS (Parentheticals) (USD $) In Thousands, except Share data, unless otherwise specified	Dec. 31, 2012	Jun. 30, 2012
Allowance for doubtful accounts (in Dollars)	$ 652	$ 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	20,798,084	20,499,861
Common stock, shares outstanding	18,481,423	18,239,941
Treasury stock, shares	2,316,661	2,259,920

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Shareholders' Equity

6 Months Ended

Dec. 31, 2012

Stockholders' Equity Note Disclosure [Text Block]

Note 3: Shareholders’ Equity

The following table sets forth shareholders’ equity and noncontrolling interest for the six months ended December 31, 2012 and 2011:

	Six Months Ended December 31,
	2012									2011
	Shareholders’ Equity			Non- Controlling			Total			Shareholders’ Equity			Non- Controlling			Total
	Zygo Corp.			Interest			Equity			Zygo Corp.			Interests			Equity
Equity, beginning of period	$	173,625		$	2,355		$	175,980		$	124,720		$	3,367		$	128,087
Net income		3,967			709			4,676			12,647			1,086			13,733
Foreign currency translation effect		261			104			365			(982	)		(261	)		(1,243	)
Total		4,228			813			5,041			11,665			825			12,490
Share based compensation		3,988			—			3,988			2,318			—			2,318
Repurchase of restricted stock		(1,078	)		—			(1,078	)		(301	)		—			(301	)
Employee Stock Purchase		15			—			15			—			—			—
Exercise of employee stock options and related tax effect		868			—			868			1,221			—			1,221
Dividends attributable to noncontrolling interests		—			(1,101	)		(1,101	)		—			(746	)		(746	)
Purchase of subsidiary shares from noncontrolling interest		(2,777	)		(378	)		(3,155	)		—			—			—
Equity, end of period	$	178,869		$	1,689		$	180,558		$	139,623		$	3,446		$	143,069

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Segment and Major Customer Information (Detail)	3 Months Ended	6 Months Ended		3 Months Ended	6 Months Ended	3 Months Ended
	Dec. 31, 2011 Customer One [Member]	Dec. 31, 2012 Customer One [Member]	Dec. 31, 2011 Customer One [Member]	Dec. 31, 2011 Customer Two [Member]	Dec. 31, 2011 Customer Two [Member]	Dec. 31, 2012 No Customer [Member]
Entity-Wide Revenue, Major Customer, Percentage	14.00%	10.00%	12.00%	11.00%	11.00%	10.00%

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Shareholders' Equity (Tables)

6 Months Ended

Dec. 31, 2012

Schedule of Stockholders Equity [Table Text Block]

The following table sets forth shareholders’ equity and noncontrolling interest for the six months ended December 31, 2012 and 2011:

	Six Months Ended December 31,
	2012									2011
	Shareholders’ Equity			Non- Controlling			Total			Shareholders’ Equity			Non- Controlling			Total
	Zygo Corp.			Interest			Equity			Zygo Corp.			Interests			Equity
Equity, beginning of period	$	173,625		$	2,355		$	175,980		$	124,720		$	3,367		$	128,087
Net income		3,967			709			4,676			12,647			1,086			13,733
Foreign currency translation effect		261			104			365			(982	)		(261	)		(1,243	)
Total		4,228			813			5,041			11,665			825			12,490
Share based compensation		3,988			—			3,988			2,318			—			2,318
Repurchase of restricted stock		(1,078	)		—			(1,078	)		(301	)		—			(301	)
Employee Stock Purchase		15			—			15			—			—			—
Exercise of employee stock options and related tax effect		868			—			868			1,221			—			1,221
Dividends attributable to noncontrolling interests		—			(1,101	)		(1,101	)		—			(746	)		(746	)
Purchase of subsidiary shares from noncontrolling interest		(2,777	)		(378	)		(3,155	)		—			—			—
Equity, end of period	$	178,869		$	1,689		$	180,558		$	139,623		$	3,446		$	143,069

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Derivatives and Hedging Activities (Tables)

6 Months Ended

Dec. 31, 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 December 31, 2012 and June 30, 2012:

Derivatives not designated as hedging instruments			Balance Sheet Location
December 31, 2012	Number of foreign exchange contracts:	12	Prepaid expenses, prepaid taxes and other current assets	$199
June 30, 2012	Number of foreign exchange contracts:	9	Prepaid expenses, prepaid taxes and other current assets	$14
			Other accrued expenses	$17

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Segment and Major Customer Information

6 Months Ended

Dec. 31, 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 segments as Metrology Solutions and Optical Systems. The 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. The 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 and six months ended December 31, 2012 and 2011:

	Three Months Ended December 31,						Six Months Ended December 31,
	2012			2011			2012			2011
Metrology Solutions
Net revenues	$	21,416		$	25,479		$	47,294		$	55,321
Gross profit	$	11,595		$	15,057		$	25,928		$	32,440
Gross margin		54	%		59	%		55	%		59	%
Optical Systems
Net revenues	$	13,219		$	14,561		$	27,547		$	28,711
Gross profit	$	3,688		$	4,585		$	6,848		$	8,819
Gross margin		28	%		31	%		25	%		31	%
Total
Net revenues	$	34,635		$	40,040		$	74,841		$	84,032
Gross profit	$	15,283		$	19,642		$	32,776		$	41,259
Gross margin		44	%		49	%		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 December 31,				Six Months Ended December 31,
	2012		2011		2012		2011
Americas	$	19,755	$	22,170	$	38,618	$	46,461
Japan		5,336		5,692		11,667		12,479
China		3,498		3,823		11,036		9,903
Europe		4,397		5,834		9,219		10,105
Pacific Rim		1,649		2,521		4,301		5,084
Total	$	34,635	$	40,040	$	74,841	$	84,032

Revenues from two customers accounted for 14% and 11% of net revenues for the three months ended December 31, 2011. No customer accounted for over 10% of our revenues for the three months ended December 31, 2012. Revenues from one customer accounted for 10% of net revenues for the six months ended December 31, 2012. Revenues from two customers accounted for 12% and 11% of net revenues for the six months ended December 31, 2011. Revenues from these customers were included in both reporting segments.