**Exhibit 31.1**

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

I, Paul K. Laikind, certify that:

1. I have reviewed this annual report on Form 10-K of MetabasisTherapeutics, Inc.;

2. Based on my knowledge, this report does not contain any untruestatement of a material fact or omit to state a material fact necessary to makethe statements made, in light of the circumstances under which such statementswere made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financialinformation included in this report, fairly present in all material respectsthe financial condition, results of operations and cash flows of the registrantas of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible forestablishing and maintaining disclosure controls and procedures (as defined inExchange Act Rules 13a-15(e) and 15d-15(e)) and internal controlover financial reporting (as defined in Exchange Act Rules 13a-15(f) and15d-15(f)) for the registrant and have:

a) designed such disclosurecontrols and procedures, or caused such disclosure controls and procedures tobe designed under our supervision, to ensure that material information relatingto the registrant, including any consolidated subsidiaries, is made known to usby others within those entities, particularly during the period in which thisreport is being prepared;

b) designed such internal control overfinancial reporting, or caused such internal control over financial reportingto be designed under our supervision, to provide reasonable assurance regardingthe reliability of financial reporting and the preparation of financialstatements for external purposes in accordance with generally acceptedaccounting principles;

c) evaluated the effectivenessof the registrant’s disclosure controls and procedures and presented in thisreport our 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 anychange in the registrant’s internal control over financial reporting thatoccurred during the registrant’s most recent fiscal quarter that has materiallyaffected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed,based on our most recent evaluation of internal control over financialreporting, to the registrant’s auditors and the audit committee of theregistrant’s board of directors (or persons performing the equivalentfunctions):

a) all significant deficienciesand material weaknesses in the design or operation of internal control overfinancial reporting which are reasonably likely to adversely affect theregistrant’s ability to record, process, summarize and report financialinformation; and

b) any fraud, whether or notmaterial, that involves management or other employees who have a significantrole in the registrant’s internal control over financial reporting.
|        |     | Date: March 12, 2007 |   | By:      | /s/ Paul K. Laikind                                            |     |     |     |
|--------|----------|----------------------|--------|----------|----------------------------------------------------------------|----------|----------|----------|
|   | * * | * *             |   | * * | Paul K. Laikind, Ph.D.,*Chief Executive Officer and President* | * * | * * | * * |

 

----