**Exhibit 31.1**

 

**CERTIFICATION**

**OF CHIEF EXECUTIVEOFFICER**

 

I, Malcolm L. Gefter, certifythat:

 

1.             I have reviewed this Amendment No. 1 on Form 10-K/A(“this report”) to the annual report on Form 10-K of PRAECIS PHARMACEUTICALSINCORPORATED;

 

2.             Based on my knowledge, this report does not contain anyuntrue statement of a material fact or omit to state a material fact necessaryto make the statements made, in light of the circumstances under which suchstatements were made, not misleading with respect to the period covered by thisreport;

 

3.             Based on my knowledge, the financial statements, andother financial information included in this report, fairly present in allmaterial respects the financial condition, results of operations and cash flowsof the registrant as of, and for, the periods presented in this report;

 

4.             The registrant’s other certifying officer and I areresponsible for establishing and maintaining disclosure controls and procedures(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrantand 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];

 

(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) Disclosedin this 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 other certifying officer and I havedisclosed, based on our most recent evaluation of internal control overfinancial reporting, to the registrant’s auditors and the audit committee ofthe registrant’s board of directors (or persons performing the equivalentfunctions):

 

(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.

 
| Date:                         | May 7, 2004 |   |
|-------------------------------|-------------|--------|
|                          |        |
| /s/ Malcolm  L. Gefter, Ph.D. |        |   |
| Malcolm L.  Gefter, Ph.D.     |        |
| Chief  Executive Officer      |        |
|                               |             |        |  |

 

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