**Exhibit31.1**

 

**CERTIFICATION**

 

**OFCHIEF 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 andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant, including its consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which thisreport is being prepared;

 

(b) [Paragraph omitted in accordance with SECtransition instructions];

 

(c) Evaluated the effectiveness of theregistrant’s disclosure controls and procedures and presented in this reportour conclusions about the effectiveness of the disclosure controls andprocedures, as of the end of the period covered by this report based on suchevaluation; and

 

(d) Disclosed in this report any change inthe registrant’s internal control over financial reporting that occurred duringthe registrant’s most recent fiscal quarter (the registrant’s fourth fiscalquarter in the case of an annual report) that has materially affected, or isreasonably likely to materially affect, the registrant’s internal control overfinancial 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 materialweaknesses in the design or operation of internal control over financialreporting which are reasonably likely to adversely affect the registrant’sability to record, process, summarize and report financial information; and

 

(b) Any fraud, whether or not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.

 

Date: November 9, 2004

 

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

 

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