**EXHIBIT 31.1**

 

CERTIFICATIONS

 

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

 

1.               I havereviewed this Amendment No. 1 to the Quarterly Report on Form 10-Q ofGenaissance Pharmaceuticals, Inc.;

 

2.               Based on myknowledge, this report does not contain any untrue statement of a material factor omit to state a material fact necessary to make the statements made, inlight of the circumstances under which such statements were made, notmisleading with respect to the period covered by this report;

 

3.               Based on myknowledge, the financial statements, and other financial information includedin this report, fairly present in all material respects the financialcondition, results of operations and cash flows of the registrant as of, andfor, the periods presented in this report;

 

4.               Theregistrant’s other certifying officer and I are responsible for establishingand maintaining disclosure controls and procedures (as defined in Exchange ActRules 13a-15(e) and 15d-15(e)) for the registrant and have:

 

a)              Designedsuch disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this report is being prepared;

 

b)             [Paragraphomitted in accordance with SEC transition instructions contained in SEC Release34-47986]

 

c)              Evaluatedthe effectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisreport based on such evaluation; and

 

d)             Disclosed inthis report any change in the registrant’s internal control over financialreporting that occurred during the registrant’s most recent fiscal quarter (theregistrant’s fourth fiscal quarter in the case of an annual report) that hasmaterially affected, or is reasonably likely to materially affect, theregistrant’s internal control over financial reporting; and

 

5.     The registrant’s othercertifying officer and I have disclosed, based on our most recent evaluation ofinternal control over financial reporting, to the registrant’s auditors and theaudit committee of the registrant’s board of directors (or persons performingthe equivalent functions):

 

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a)              Allsignificant deficiencies and material weaknesses in the design or operation ofinternal control over financial reporting which are reasonably likely toadversely affect the registrant’s ability to record, process, summarize andreport financial information; and

 

b)             Any fraud,whether or not material, that involves management or other employees who have asignificant role in the registrant’s internal control over financial reporting.

 
|                                      |   | /s/  Kevin Rakin                       |
|-------------------------------------------|--------|----------------------------------------|
| Date:   February  11, 2004 |   | Kevin  Rakin                           |
|                                      |   | President  and Chief Executive Officer |

 

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