<PAGE>

                                                                    EXHIBIT 31.1

                        CERTIFICATION OF PERIODIC REPORT

I, Charles D. Johnston, certify that:

    1. I have reviewed this annual report on Form 10-KSB of QualMark Corporation
       (the "small business issuer");

    2. Based on my knowledge, this report does not contain any untrue statements
       of 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 small business issuer as of, and for, the periods presented in this
       report;

    4. The small business issuer'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 small business issuer 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 small business
       issuer, 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) [Paragraph omitted in accordance with SEC transition instructions
       contained in SEC release 34-47986.]

       c) Evaluated the effectiveness of the small business issuer'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 small business issuer's
       internal control over financial reporting that occurred during the small
       business issuer's most recent fiscal quarter that has materially
       affected, or is reasonably likely to materially affect, the small
       business issuer's internal control over financial reporting; and

    5. The small business issuer's other certifying officer and I have
       disclosed, based on our most recent evaluation of internal control over
       financial reporting, to the small business issuer's auditors and the
       audit committee of small business issuer's board of directors (or persons
       performing the equivalent function):

       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 small business issuer'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 small business issuer's
       internal control over financial reporting.

Date:  March 26, 2004

                                         /s/ Charles D. Johnston
                                         ---------------------------------------
                                         Charles D. Johnston
                                         President & Chief Executive Officer