<Page>
                                                                    EXHIBIT 31.1

                          CERTIFICATION OF DISCLOSURE

                       IN THE REGISTRANT'S ANNUAL REPORT

    I, J. Bruce Robinson, certify that:

        1) I have reviewed this annual report on Form 10-K of Zygo Corporation;

        2) Based on my knowledge, this annual 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 annual report;

        3) Based on my knowledge, the financial statements, and other financial
    information included in this annual 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 annual 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)) 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 annual report is
       being prepared;

           b) Evaluated the effectiveness of the registrant's disclosure
       controls and procedures and presented in this annual report our
       conclusions about the effectiveness of the disclosure controls and
       procedures, as of the end of the period covered by this annual report
       based on such evaluation; and

           c) Disclosed in this annual 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):

           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.

<Table>
<S>                                            <C>
Date: September 24, 2003                                  /s/ J. BRUCE ROBINSON
                                               ................................................
                                                              J. Bruce Robinson
                                               Chairman, President, and Chief Executive Officer
</Table>