QuickLinks -- Click here to rapidly navigate through this document
EXHIBIT 23.1
CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
We consent to the incorporation by reference into Registration Statement Nos. 333-152483, 333-152970, 333-153434 and 333-139679 on Form S-3 and into Registration Statement No. 333-145704 on Form S-8 of CombiMatrix Corporation of our report dated March 16, 2009, on our audit of the consolidated financial statements of CombiMatrix Corporation as of and for the year ended December 31, 2008.
Our report, dated March 16, 2009, contains an explanatory paragraph that states that CombiMatrix Corporation has a history of incurring net losses and net operating cash flow deficits. These conditions raise substantial doubt about the Company's ability to continue as a going concern. The consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty.
/s/ PETERSON SULLIVAN LLP
March 27, 2009
Seattle, Washington
QuickLinks
CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM