Exhibit 99.1

TRIUS THERAPEUTICS REPORTS 2012 THIRD QUARTER FINANCIAL RESULTS

San Diego, CA, November 5, 2012 – Trius Therapeutics, Inc. (Nasdaq: TSRX), a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for life-threatening infections, announced today its financial results for the third quarter ended September 30, 2012 and provided an update on recent key events.

At September 30, 2012, Trius had cash, cash equivalents and investments totaling $70.9 million.

For the third quarter of 2012, Trius reported a net loss of $17.7 million versus net income of $14.3 million in the comparable period in 2011. For the nine months ended September 30, 2012, Trius reported a net loss of $39.7 million compared to $5.7 million for the same period in 2011. The net loss during the three and nine months ended September 30, 2012 was largely due to clinical and nonclinical development activities for tedizolid phosphate, our lead investigational drug in Phase 3 clinical development. For the third quarter of 2012, Trius reported a net loss per share of $0.46 versus earnings per share of $0.50 in the third quarter of 2011. For the nine months ended September 30, 2012 and 2011, Trius reported a net loss per share of $1.06 and $0.22, respectively. The increase in the net loss per share was primarily due to the fact that the Company received an upfront payment of $25.0 million in the comparable period in the prior year upon entering into a collaboration and license agreement with Bayer Pharma AG (Bayer), but received no similar payments in the third quarter of the current year. Aside from this one-time payment, the increase in the net loss per share for both the three month and nine months ended September 30, 2012 was largely due to higher clinical and nonclinical development expenses for tedizolid phosphate offset by an increase in shares outstanding resulting from our follow on offering in January 2012.

Revenues for the three months ended September 30, 2012 were $6.0 million compared to $30.4 million for the same period in 2011. For the nine months ended September 30, 2012, revenues were $22.0 million compared to $36.0 million for the same period in 2011. The decrease in revenues during the three and nine months ended September 30, 2012 was due to the $25.0 million upfront payment received from Bayer in 2011. Excluding this one-time payment, revenues for the third quarter and nine months ended September 30, 2012 increased $0.5 million and $11.0 million, respectively, primarily due to sponsored development activities and milestone payments from our collaboration with Bayer as a result of the continued progress of our development program for tedizolid phosphate.

Research and development expenses for the three months ended September 30, 2012 were $19.3 million compared to $14.9 million for the same period in 2011. For the nine months ended September 30, 2012 and 2011, research and development expenses were $52.6 million and $35.7 million, respectively. The increase in research and development expenses was primarily related to higher clinical trial and development costs for tedizolid phosphate.

General and administrative expenses for the three months ended September 30, 2012 increased to $4.4 million compared to $3.7 million for the same period in 2011. For the nine months ended September 30, 2012 and 2011, general and administrative expenses were $10.7 million and $8.6 million, respectively. The increase in general and administrative expenses was primarily due to an increase in pre-commercialization activities in 2012 as well as additional personnel costs due to increased headcount in 2012.

As of November 1, 2012, Trius had 39,406,671 shares outstanding.

Program Updates & Upcoming Events

Trius continued enrollment in the second Phase 3 clinical trial of tedizolid phosphate, the ESTABLISH-2 (TR-701-113) study, for acute bacterial skin and skin structure infections, or ABSSSI, and the study remains on track to report top line data in early 2013. The Company plans to initiate a Phase 3 program for the treatment of pneumonia in the first half of 2013 using the same 200 mg, once daily dose of tedizolid phosphate that is currently being tested to treat skin infections. In addition, the Company is progressing with IND-enabling studies funded by a contract with the National Institute of Allergy and Infectious Diseases, or NIAID, for its Gyrase-B development candidate with potent activity against Gram-negative and Gram-positive bacterial pathogens. A Phase 1 clinical trial is expected to start in 2013.

About Trius Therapeutics

Trius Therapeutics, Inc. is a biopharmaceutical company focused on the discovery, development and commercialization of innovative antibiotics for life-threatening infections. The Company’s lead investigational drug, tedizolid phosphate, is a once daily, IV and orally administered second generation oxazolidinone in Phase 3 clinical development for the treatment of ABSSSI and serious Gram-positive

infections, including those cause by methicillin-resistant staphylococcus aureus (MRSA). Trius has two Special Protocol Assessments with the FDA for its two Phase 3 ABSSSI trials and has partnered with Bayer HealthCare for the development and commercialization of tedizolid phosphate outside of the U.S., Canada and the European Union. In addition to the Company’s tedizolid phosphate clinical program, Trius has initiated IND-enabling studies for its Gyrase-B development candidate with potent activity against Gram-negative bacterial pathogens including multi-drug resistant strains of E. coli, Klebsiella, Acinetobacter and Pseudomonas. The Gyrase-B program is one of the two preclinical programs supported by federal contracts. For more information, visit www.triusrx.com.

Forward-Looking Statements

Statements contained in this press release regarding matters that are not historical facts are “forward-looking statements” within the meaning of the Private Securities Litigation Reform Act of 1995. Because such statements are subject to risks and uncertainties, actual results may differ materially from those expressed or implied by such forward-looking statements. Such statements include, but are not limited to, statements regarding Trius’ ability to successfully complete its ongoing clinical trials and development programs. Risks that contribute to the uncertain nature of the forward-looking statements include: the accuracy of Trius’ estimates regarding expenses, future revenues and capital requirements; the success and timing of Trius’ preclinical studies and clinical trials; regulatory developments in the United States and foreign countries; changes in Trius’ plans to develop and commercialize its product candidates; Trius’ ability to obtain additional financing; Trius’ ability to obtain and maintain intellectual property protection for its product candidates; and the loss of key scientific or management personnel. These and other risks and uncertainties are described more fully in Trius’ most recently filed SEC documents, including its Form 10-K, Forms 10-Q and other documents filed with the United States Securities and Exchange Commission, including those factors discussed under the caption “Risk Factors” in such filings. All forward-looking statements contained in this press release speak only as of the date on which they were made. Trius undertakes no obligation to update such statements to reflect events that occur or circumstances that exist after the date on which they were made.

Trius Therapeutics, Inc.

Statements of Operations

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Trius Therapeutics, Inc.

Balance Sheets

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