**Exhibit 31.1**

 

**CERTIFICATIONOF PRINCIPAL EXECUTIVE OFFICER**

 

I, Michael N. Chang,certify that:

 

1. I have reviewed thisquarterly report on Form 10-Q of Optimer Pharmaceuticals, Inc.;

 

2. Based on my knowledge,this report does not contain any untrue statement of a material fact or omit tostate a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading withrespect to the period covered by this report;

 

3. Based on my knowledge,the financial statements, and other financial information included in thisreport, fairly present in all material respects the financial condition,results of operations and cash flows of the registrant as of, and for, theperiods presented in this report;

 

4. The registrant’s othercertifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and15d-15(e)) and internal control over financial reporting (as defined inExchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant andhave:

 

a)              designed such disclosure controls and procedures, orcaused such disclosure controls and procedures to be designed under oursupervision, to ensure that material information relating to the registrant,including its consolidated subsidiaries, is made known to us by others withinthose entities, particularly during the period in which this report is beingprepared;

 

b)             designed such internal control over financialreporting, or caused such internal control over financial reporting to bedesigned under our supervision, to provide reasonable assurance regarding thereliability of financial reporting and the preparation of financial statementsfor external purposes in accordance with generally accepted accountingprinciples;

 

c)              evaluated the effectiveness of the registrant’sdisclosure controls and procedures and presented in this report our conclusionsabout the effectiveness of the disclosure controls and procedures, as of theend of the period covered by this report based on such evaluation; and

 

d)             disclosed in this report any change in the registrant’sinternal control over financial reporting that occurred during the registrant’smost recent fiscal quarter (the registrant’s fourth fiscal quarter in the caseof an annual report) that has materially affected, or is reasonably likely tomaterially affect, the registrant’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):

 

a)              all significant deficiencies and material weaknessesin the design or operation of internal control over financial reporting whichare reasonably likely to adversely affect the registrant’s ability to record,process, summarize and report financial information; and

 

b)             any fraud, whether or not material, that involvesmanagement or other employees who have a significant role in the registrant’sinternal control over financial reporting.

 

Date: May 8, 2008

 
| /s/ Michael N. Chang                   |   |
|----------------------------------------|--------|
| Michael N. Chang                       |   |
| President and Chief  Executive Officer |   |

 

----