**Exhibit 31.2**

 

**CERTIFICATION OF PRINCIPAL FINANCIAL OFFICER**

**PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACTOF 2002**

 

I, John D. Prunty, certifythat:

 

1. I have reviewed thisannual report on Form 10-K/A 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. [Intentionally omitted];

 

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 registrantand  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)        designedsuch internal control over financial reporting, or caused such internal controlover financial reporting to be designed under our supervision, to providereasonable assurance regarding the reliability of financial reporting and thepreparation of financial statements for external purposes in accordance withgenerally accepted accounting principles;

 

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 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 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: April 1, 2009                      |
|-----------------------------------------------|
|                                          |
| /s/ John D. Prunty                            |   |
| John D. Prunty                                |
| Vice-President and Chief  Financial Officer   |
| (Principal Financial and  Accounting Officer) |

 

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