<PAGE>

                                                                    EXHIBIT 31.1

                                 CERTIFICATION

I, Daniel S. Lynch, Acting Chief Executive Officer of ImClone Systems
Incorporated, certify that:

          1.  I have reviewed this quarterly report on Form 10-Q for the Quarter
     Ended September 30, 2003 of ImClone Systems Incorporated;

          2.  Based on my knowledge, this quarterly 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 quarterly report;

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

             b) [Reserved]

             c) evaluated the effectiveness of the registrant's disclosure
        controls and procedures and presented in this quarterly 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 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.

                                                  /s/ DANIEL S. LYNCH
                                          --------------------------------------
                                                     Daniel S. Lynch
                                              Acting Chief Executive Officer

Date: November 12, 2003