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

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|I, Chris L. Koliopoulos,
 certify that:
|                                        |                                                                                                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                                                                                                                                                
|1)                                      | I have reviewed this
 quarterly report on Form 10-Q of Zygo Corporation;                                                                                                                                                                                                                                                                    
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|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: November 9, 2012 |                                        | 
|                       |                                        | 
|                       | /s/ Chris L. Koliopoulos               | 
|                       |                                        | 
|                       | Chris L. Koliopoulos                   | 
|                       | President and Chief
 Executive Officer

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