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|UNITED STATES
 SECURITIES AND EXCHANGE COMMISSION
|Washington,
 D.C. 20549                          
|                                                 
|FORM 10-Q/A                                      
|AMENDMENT No. 1                                  

(Mark One)


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|x                                                                                                           | QUARTERLY
 REPORT PURSUANT TO SECTION 13 OR 15(d)OF THE SECURITIES EXCHANGE ACT OF 1934  
|                                                                                                            |                                                                                          
|For the
 quarterly period ended September 30, 2010                                                          |                                                                                          
|                                                                                                            |                                                                                           | 
|                                                                                                            | 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).
(1)          o YES o NO

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

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

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

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.

17,569,511 shares of Common Stock, $.10 Par
Value, at November 1, 2010


(1) The
registrant is not currently required to submit Interactive Data Files pursuant
to Rule 405 of Regulation S-T.


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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 are intended to 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, plans, strategy,
project, and other words of similar meaning in connection with a discussion
of 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 net revenues
to our major customers; manufacturing and supplier 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 the reorganization of our
business; 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; risks related to recent
business acquisitions, including the acquisition of substantially all the
assets of ASML US, Incs Richmond, California facility and integration of the
businesses and employees; the risk related to the Companys recent changes to
senior management; and the risks associated with the recovery from the recent
earthquake, tsunami and nuclear disaster in Japan and its impact on our
customers, suppliers, and operations.

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 occurring
after the date of this Form 10-Q. 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 (the Commission), including
our Form 10-K for the fiscal year ended June 30, 2010.

EXPLANATORY NOTE

This Amendment
No. 1 on Form 10-Q/A (this Form 10-Q/A) of Zygo Corporation amends our
Quarterly Report on Form 10-Q for the quarterly period ended September 30, 2010,
initially filed with the Commission on November 9, 2010 (the Initial Filing).
Specifically, this Form 10-Q/A amends Item 4, Controls and Procedures, as the
disclosure in Item 4, Controls and Procedures included within the Initial
Filing did not provide a conclusion regarding Managements evaluation of the
effectiveness of Zygos disclosure controls and procedures. The Initial Filing,
as amended by this Form 10-Q/A, is referred to herein as this Form 10-Q.

In addition,
this Form 10-Q/A has been amended to contain currently dated certifications from
our Chief Executive Officer and Chief Financial Officer, as required by
Sections 302 and 906 of the Sarbanes-Oxley Act of 2002. The currently dated
certifications of our Chief Executive Officer and Chief Financial Officer are
attached to this Form 10-Q/A as Exhibits 31.1, 31.2, 32.1 and 32.2. Except as
described above, no other changes are made to the Initial Filing, and this Form
10-Q/A does not amend, update or change any other Item or the disclosures in the
Initial Filing in any way. This Form 10-Q/A does not reflect events occurring
after the filing of the Initial Filing or modify or update those disclosures
affected by subsequent events, except that the above noted certifications are
being made by our Chief Executive Officer and current Chief Financial Officer,
who commenced employment with the company on February 17, 2011.

2

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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
our management necessarily was required to apply its judgment in evaluating the
cost-benefit relationship of possible controls and procedures.

We identified
a material weakness on May 10, 2010 related to inadequate controls regarding
our accounting for unusual or complex transactions and, subsequently, concluded
that our internal control over financial reporting was not effective at June
30, 2010. We began the process of implementing additional controls in our
financial reporting process in the fourth quarter of fiscal 2010 and continuing
into the first quarter of fiscal 2011, including adding control processes to
aid in identifying transactions that might have unusual or complex accounting
issues, a process to enhance our analysis of accounting for unusual or complex
transactions as they arise in accordance with accounting principles generally
accepted in the United States of America, and have added external accounting
resources to review our accounting for unusual or complex transactions.
However, as of the filing of our Initial Filing for the period ended
September 30, 2010, certain controls designed and implemented to address the identified
material weakness in the period-end financial reporting process had not had a
sufficient period of time to operate for our management to conclude that they
were operating effectively at September 30, 2010.

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 September 30, 2010), 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, that 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 that occurred in the most recent fiscal quarter (the quarter ended
September 30, 2010) that materially affected, or are reasonably likely to
materially affect, our internal control over financial reporting.

3

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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                                            

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                            
|                   | Chairman,
 President, and Chief Executive Officer
|                   |                                                  
|                   |                                                  
|                   | /s/ John P.
 Jordan                              
|                   |                                                   | 
|                   | John P.
 Jordan                                  
|                   | Vice
 President and Chief Financial Officer      
|                   |                                                  
|Date: May 10, 2011

4

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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                                            

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