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                                                                   EXHIBIT 31.1

                                 CERTIFICATIONS

I, Kevin Rakin, President and Chief Executive Officer of Genaissance
Pharmaceuticals, Inc., certify that:

1.  I have reviewed this Amendment No. 2 to the Annual Report on Form 10-K of
    Genaissance Pharmaceuticals, Inc.;

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)) 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 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 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 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

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        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.

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Dated: February 11, 2004                          /s/ KEVIN RAKIN
                                                  -------------------------------------------
                                                  Kevin Rakin
                                                  President and Chief Executive Officer
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