**Exhibit31.1**

 

**CERTIFICATION**

**OF CHIEF EXECUTIVE OFFICER**

 

I, Malcolm L. Gefter, certify that:

 

1.                                       Ihave reviewed this quarterly report on Form 10-Q of PRAECIS PHARMACEUTICALSINCORPORATED;

 

2.                                       Basedon my knowledge, this report does not contain any untrue statement of amaterial fact or omit to state a material fact necessary to make the statementsmade, in light of the circumstances under which such statements were made, notmisleading with respect to the period covered by this report;

 

3.                                       Basedon my knowledge, the financial statements, and other financial informationincluded in 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) Designed such disclosure controls and procedures, or caused suchdisclosure controls and procedures to be designed under our supervision, toensure that material information relating to the registrant, including itsconsolidated 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];

 

(c) Evaluated the effectiveness of the registrant’s disclosure controlsand procedures and presented in this report our conclusions about theeffectiveness of the disclosure controls and procedures, as of the end of theperiod covered by this report based on such evaluation; and

 

(d) Disclosed in this report any change in the registrant’s internalcontrol over financial reporting that occurred during the registrant’s mostrecent fiscal quarter (the registrant’s fourth fiscal quarter in the case of anannual report) that has materially affected, or is reasonably likely tomaterially affect, the registrant’s internal control over financial reporting;and

 

5.                                       Theregistrant’s other certifying officer and I have disclosed, based on our mostrecent evaluation of internal control over financial reporting, to theregistrant’s auditors and the audit committee of the registrant’s board ofdirectors (or persons performing the equivalent functions):

 

(a) All significant deficiencies and material weaknesses in the designor operation of internal control over financial reporting which are reasonablylikely 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 orother employees who have a significant role in the registrant’s internal controlover financial reporting.

 

Date: May 10, 2004

 

 
| /s/ Malcolm L. Gefter, Ph.D. |   |
|------------------------------|--------|
| Malcolm L. Gefter, Ph.D.     |
| Chief Executive Officer      |

 

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