EXHIBIT
31.1

CERTIFICATION
OF DISCLOSURE
IN THE REGISTRANTS REPORT

I, J. Bruce Robinson, certify that:

1) I have reviewed this 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 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;         
| |                                                                                                                                                                                                                                                                                                                                                                                                     
| | 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 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
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
| |                                                                                                                                                                                                                                                                                   
| | 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 7, 2006

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

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