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, J. Bruce
Robinson, certify that:

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|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;                               
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|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;                                                  
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|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:

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| | 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;         
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| | 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;                
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| | 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                                                                                                      
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| | 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

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|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):

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| | 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
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| | 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, 2006

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| | /s/ J. Bruce
  Robinson   
| |                           
| | J. Bruce
  Robinson       
| | Chairman,
  President, and
| | Chief
  Executive Officer 

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