**EXHIBIT 31.1**

 

**CERTIFICATION OF CHIEF EXECUTIVE OFFICER**

** **

I,Amit Kumar, certify that:

 
|   | 1.     | I  have reviewed this Quarterly Report on Form 10-Q of CombiMatrix Corporation;                                                                                                                                                                                                                                   |
|--------|--------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|   |   |                                                                                                                                                                                                                                                                                                              |
|   | 2.     | Based on my knowledge, this report does not contain any untrue  statement of a material fact or omit to state a material fact necessary to  make the statements made, in light of the circumstances under which such  statements were made, not misleading with respect to the period covered by  this report;    |
|   |   |                                                                                                                                                                                                                                                                                                              |
|   | 3.     | Based on my knowledge, the financial statements, and other financial  information included in this report, fairly present in all material respects  the financial condition, results of operations and cash flows of the  registrant as of, and for, the periods presented in this report;                        |
|   |   |                                                                                                                                                                                                                                                                                                              |
|   | 4.     | The registrant’s other certifying officer and I are responsible for  establishing and maintaining disclosure controls and procedures (as defined  in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:                                                                                |
|   |   |                                                                                                                                                                                                                                                                                                              |
|   |   | a.                                                                                                                                                                                                                                                                                                                | Designed such disclosure controls and procedures, or caused such  disclosure controls and procedures to be designed under our supervision, to  ensure that material information relating to the registrant, including its  consolidated subsidiaries, is made known to us by others within those  entities, particularly during the period in which this report is being  prepared; |
|   |   |                                                                                                                                                                                                                                                                                                              |   |
|   |   | b.                                                                                                                                                                                                                                                                                                                | [intentionally  omitted] |
|   |   |                                                                                                                                                                                                                                                                                                              |   |
|   |   | c.                                                                                                                                                                                                                                                                                                                | Evaluated the effectiveness of the registrant’s disclosure controls  and procedures and presented in this report our conclusions about the  effectiveness of the disclosure controls and procedures, as of the end of the  period covered by this report based on such evaluation; and |
|   |   |                                                                                                                                                                                                                                                                                                              |   |
|   |   | d.                                                                                                                                                                                                                                                                                                                | Disclosed in this report any change in the registrant’s internal  control over financial reporting that occurred during the registrant’s most  recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of  an annual report) that has materially affected, or is reasonably likely to  materially affect, the registrant’s internal 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 financial reporting,  to the registrant’s auditors and the audit committee of the registrant’s  board of directors (or persons performing the equivalent functions): |
|   |   |                                                                                                                                                                                                                                                                                                              |   |
|   |   | a.                                                                                                                                                                                                                                                                                                                | All significant deficiencies and material weaknesses in the design or  operation of internal control over financial reporting which are 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 involves management or other  employees who have a significant role in the registrant’s internal control  over financial reporting. |

 

 
| Dated:   November 7, 2007 | /s/ Amit Kumar                                                                   |
|--------------------------------|----------------------------------------------------------------------------------|
|                           | **Amit Kumar*****Chief Executive  Officer******(Principal Executive  Officer)*** |

 

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