Trius Therapeutics is developing novel anti-infective compounds to treat serious bacterial infections. Their lead product candidate, tedizolid phosphate, is completing Phase 3 clinical trials for the treatment of acute bacterial skin and skin structure infections. Tedizolid has shown high efficacy comparable to generic antibiotics with a better safety profile in Phase 3 trials, including significantly lower impacts on platelets and rates of adverse gastrointestinal events. If approved, tedizolid would provide an important new treatment option with IV or oral dosing for patients with these infections. Trius is also advancing a new class of antibiotics targeting bacterial gyrase through their preclinical pipeline.

1. The Future of Anti-Infectives
Baird Healthcare Conference
September 5, 2012
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2. Forward looking statements
Statements made in this presentation 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, the expected timing for reporting of top-line data for the TR701-113 study,
Trius’ ability to obtain regulatory approval for tedizolid, market penetration and acceptance of
tedizolid and the initiation of clinical studies for Trius’ Gyrase B program. Risks that contribute to the
uncertain nature of the forward-looking statements include: Trius’ future preclinical studies and
clinical trials may not be successful; changes in regulatory requirements in the United States and
foreign countries may prevent or significantly delay regulatory approval of Trius’ products; Trius may
change its plans to develop and commercialize its product candidates; the FDA may not agree with
Trius’ interpretation of the data from recently-completed clinical trials of tedizolid; Trius may
decide, or the FDA may require Trius, to conduct additional clinical trials or to modify Trius’ ongoing
clinical trials; Trius may experience delays in the commencement, enrollment, completion or analysis
of clinical testing for its product candidates, or significant issues regarding the adequacy of its
clinical trial designs or the execution of its clinical trials, which could result in increased costs and
delays, or limit Trius’ ability to obtain regulatory approval; the third parties with whom Trius has
partnered with for the development of tedizolid and upon whom Trius relies to conduct its clinical
trials and manufacture its product candidates may not perform as expected; tedizolid may not
receive regulatory approval or be successfully commercialized; unexpected adverse side effects or
inadequate therapeutic efficacy of tedizolid could delay or prevent regulatory approval or
commercialization; Trius’ may be unable to obtain and maintain intellectual property protection for
its product candidates; the loss of key scientific or management personnel; Trius’ ability to obtain
additional financing; and the accuracy of Trius’ estimates regarding expenses, future revenues and
capital requirements. These and other risks and uncertainties are described more fully in Trius’ most
recent 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.
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3. Investment highlights
• Focus on novel antibacterial compounds for serious infections
• Tedizolid completing confirmatory ESTABLISH-2 Phase 3 trial
– ESTABLISH-1 trial met all primary and secondary endpoints
– NDA filing for acute bacterial skin and skin structure infections
(ABSSSI) expected 2H 2013
– De-risked asset with high efficacy, strong safety, and convenience
– Additional opportunities in lung and blood stream infections
• Broad spectrum gyrase program entering clinic in 2013
• Significant potential near-term catalysts
• Strong balance sheet
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4. Trius pipeline
Pre-clinical Phase 1 Phase 2 Phase 3
Tedizolid Phosphate
Oral
ABSSSI
IV/Oral
HAP/VAP IV
Bacteremia IV/Oral
GyrB/ParE
Gram- Infections IV
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5. Strong growth in MRSA* treatment days
Total hospital treatment days in US
(Vancomycin, Linezolid and Daptomycin)
25.8M
24.0M
22.2M
21.1M 21.0M
16.7M
2005 2006 2007 2008 2009 2010
Source: AMR (United States market) *methicillin-resistant Staphylococcus aureus 5

6. Increasing resistance to vancomycin
Resistance of MRSA against Vancomycin
11.1%
9.2%
3.8%
3.3%
2.8%
2005 2006 2007 2008 2009
Source: Theravance Company Report, April 2010 & AMR (United States market).
AMR - Hospital Insight Series, US Data, August 2011 6

7. Physician attitude on vancomycin is changing
Percent of physicians reporting decreased or increased perscriptions
51%
39%
More
9%
8% 6%
Less
48%
Vancomycin Zyvox Cubicin
Source: AMR - Hospital Insight Series, US Data, August 2011
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8. Tedizolid: highly differentiated oxazolidinone
Tedizolid Linezolid (Zyvox)
Week 1 Week 2 Week 1 Week 2
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9. Strong product profile
Generic
Attribute Linezolid Vancomycin Daptomycin Tedizolid
IV/Oral
 X X 
In-Vivo Bactericidal X   
Active in Lung
Infections   X 
Once Daily
Treatment X X  

Short Course of
Therapy X X X
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10. Phase 3 trial design: ESTABLISH-1 (oral), ESTABLISH-2 (IV/PO)
Safety Analysis
Tedizolid
1x 200mg Placebo
n=667 Post-Treatment Evaluations
Linezolid
2x 600mg
1o 2o 1o 2o
FDA FDA EMA EMA
END-POINTS FOR GLOBAL REGISTRATION
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11. 1o endpoint achieved: current & expected guidance
79.5%
79.4%
78.0%
Tedizolid
76.1%
Linezolid
Current Guidelines* Expected Guidelines**
Lesion Criteria (Area) Lesion Criteria (Area)
No increase from baseline ≥20% reduction from baseline
Fever Criteria (Temperature) Fever Criteria (Temperature)
Measurements required Excluded*
* Primary endpoint as agreed to under Study 112 and 113 SPA
** FNIH recommendations to FDA: ABSSSI Docket ID: FDA-2010-D-0433 11

12. Significantly lower impact on platelets
75% - 100% LLN (112-150K/μL)
<75% LLN (<112K/μL)
14.9%*
9.2%*
4.9%
2.3%
Linezolid Tedizolid
* Statistically significant difference
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13. Phase 3: lower rates of adverse events
Linezolid Tedizolid
43.3%
40.8%
31.0%
24.2% 25.4%
16.3%*
Any TEAE Drug-Related TEAE GI Disorder
TEAE = Treatment Emergent Adverse Event
Gastrointestinal AEs incl. diarrhea, nausea, vomiting & dyspepsia
* Statistically significant difference: p = 0.004
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14. Tedizolid on track toward market
• Enrollment of ESTABLISH-2 trial (IV > PO) on track
• Expected top line data H1 2013
• Expected NDA filing H2 2013
• Potential NDA approval mid 2014*
* With Priority Review afforded by the GAIN Act
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15. Upcoming catalysts and milestones
ogramEvent Timing
Present Abstracts at ICAAC Sep 2012
Top-line Data - 2nd Phase 3 in ABSSSI H1 2013
Tedizolid
File NDA H2 2013
Potential European Partnership 2012/13
Potential U.S. Launch 2014
Gyrase
Present Abstracts at ICAAC Sep 2012
File IND/Initiate Phase 1 2013
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16. Capitalization
Cash and Marketable Securities (6/30/12) $84M
Long-term Debt (6/30/12) $0M
Shares Outstanding (8/1/12) 38.8M
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17. Investment highlights
• Focus on novel antibacterial compounds for serious infections
• Tedizolid completing confirmatory ESTABLISH-2 Phase 3 trial
– ESTABLISH-1 trial met all primary and secondary endpoints
– NDA filing for acute bacterial skin and skin structure infections
(ABSSSI) expected 2H 2013
– De-risked asset with high efficacy, strong safety, and convenience
– Additional opportunities in lung and blood stream infections
• Broad spectrum gyrase program entering clinic in 2013
• Significant potential near-term catalysts
• Strong balance sheet
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18. The Future of Anti-Infectives
Baird Healthcare Conference
September 5, 2012
18