**Exhibit 31.1**

 

**CERTIFICATION OF CHIEF EXECUTIVE OFFICER PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002**

 

I, Paul K.Laikind, certify that:

 

1. I have reviewedthis report on Form 10-Q of Metabasis Therapeutics, Inc.;

 

2. Based on myknowledge, this report does not contain any untrue statement of a material factor omit to state a material fact necessary to make the statements made, inlight of the circumstances under which such statements were made, notmisleading with respect to the period covered by this report;

 

3. Based on myknowledge, the financial statements, and other financial information includedin 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. The registrant’sother certifying 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) and15d-15(f), for the registrant and have:

 

a)designed such disclosure controls and procedures, or caused such disclosurecontrols and procedures to be designed under our supervision, to ensure thatmaterial information relating to the registrant, including any consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this report is being prepared;

 

b)designed such internal control over financial reporting, or caused suchinternal control over financial reporting to be designed under our supervision,to provide reasonable assurance regarding the reliability of financialreporting and the preparation of financial statements for external purposes inaccordance with generally accepted accounting principles;

 

c)evaluated the effectiveness of the registrant’s disclosure controls andprocedures and presented in this report our conclusions about the effectivenessof the disclosure controls and procedures, as of the end of the period coveredby this report based on such evaluation; and

 

d)disclosed in this report any change in the registrant’s internal control overfinancial reporting that occurred during the registrant’s most recent fiscalquarter (the registrant’s fourth fiscal quarter in the case of an annualreport) that has materially affected, or is reasonablylikely to materially affect, the registrant’s internal control over financialreporting; and

 

5. The registrant’sother certifying officer and I have disclosed, based on our most recentevaluation of internal control over financial reporting, to the registrant’sauditors and the audit committee of the registrant’s board of directors (orpersons performing the equivalent functions):

 

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 managementor other employees who have a significant role in the registrant’s internalcontrol over financial reporting.

 
|   | Date: November 10,  2008 | By:    | /s/ Paul K. Laikind                                |
|--------|-------------------------------|--------|----------------------------------------------------|
|   |                          |   | Paul K. Laikind, Ph.D.,  *Chief Executive Officer* |

 

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