Exhibit 23.2

Consent of Independent Registered Public Accounting Firm

We consent to the reference to our firm under the caption “Experts” in the Registration Statement (Form S-3) and related Prospectus of Trius Therapeutics, Inc. for the registration of shares of its Common Stock, Preferred Stock, Debt Securities and Warrants and to the incorporation by reference therein of our reports dated March 14, 2012, with respect to the financial statements of Trius Therapeutics, Inc., and the effectiveness of internal control over financial reporting of Trius Therapeutics, Inc., included in its Annual Report (Form 10-K) for the year ended December 31, 2011, filed with the Securities and Exchange Commission.

/s/ Ernst & Young LLP

San Diego, California

August 31, 2012