<Page>

                                                                    EXHIBIT 31.1

             CERTIFICATION PURSUANT TO RULES 13a-14(a) AND 15d-14(a)
        UNDER THE SECURITIES EXCHANGE ACT OF 1934 AS ADOPTED PURSUANT TO
                  SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002

I, Patrick J. Sullivan, certify that:

     1.   I have reviewed this annual report on Form 10-K of Cytyc 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 fourth fiscal quarter 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 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: January 30, 2004              /s/ Patrick J. Sullivan
                                    -----------------------
                                    Patrick J. Sullivan
                                    Chief Executive Officer and President