The document discusses Trius Therapeutics' pipeline of anti-infective drugs, focusing on tedizolid phosphate and its gyrase B/ParE program. Tedizolid completed a positive Phase 3 trial for acute bacterial skin and skin structure infections and is currently in a confirmatory Phase 3 trial. If approved, it could shift market share from generic vancomycin and linezolid due to its efficacy against resistant pathogens and improved safety profile. The gyrase program is set to enter clinical trials in 2013. Trius has sufficient cash reserves and expects key clinical data readouts and regulatory filings in the near future.

1. The Future of Anti-Infectives
2012 Credit Suisse Healthcare Conference
November 14, 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
– De-risked asset with high efficacy & superior safety
• Bayer collaboration to generate additional clinical data
• Broad spectrum gyrase program entering clinic in 2013
• Significant potential near-term catalysts
3

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
4

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 prescriptions
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
8

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. Tedizolid Attributes Align Well With Market Need
Key unmet needs for antibacterials
Activity against Gram-
negative pathogens
Increasing level of importance
Activity against
resistant pathogens
Improved safety and
tolerability profile
Shorter treatment
Tedizolid
courses
Lower cost of
therapy
Oral/IV switch
Source: Datamonitor. 10

11. Tedizolid Profile Shifts Share From Both Vancomycin and Zyvox
Allocation of Common Agents for Treatment of MRSA Overall
(n=165)
Original
Allocation
50% 12% 21% 7% 8% 3%
50%
38%
% Patients Prescribed
29%
Future Usage
11%
9%
5% 6%
3%
-2pp 0pp
-3pp -2pp
Change from
-12pp -10pp
Current
-25%
Tedizolid Vancomycin Cubicin Zyvox Teflaro Tygacil Other
D13: Now, please think about your prescribing for these same patients if Product X were also available, considering the fact that trials would be
Trius Quantitative Study, 2012 ongoing for hospital-acquired pneumonia at the time Product X becomes available. 11

12. Generic Linezolid Has a Modest Impact on Tedizolid
Impact of Generic Linezolid on Treatment of MRSA ABSSSI
(n=165)
50%
40%
38%
Branded Zyvox: Tedizolid Cost per Day of Therapy Same as Zyvox
% Physicians
Generic Linezolid: Tedizolid Cost per Day of Therapy Same as Zyvox
29%
23%
14%
11%
7% 7% 6% 5% 5%
5% 5% 2%
3%
0%
Tedizolid Generic Linezolid Vancomycin Cubicin Zyvox Teflao Tygacil Other
C2: Now, please think about your prescribing for these same patients if Product X were also available, using your previous answers as a
reference.
E3: How would the availability of generic linezolid impact your use of Product X in your next 20 MRSA ABSSSI patients at that point? Please
Trius Quantitative Study, 2012 assume that the price of Product X would be the same as branded Zyvox (linezolid) per day. 12

13. Phase 3 trial design: ESTABLISH-1 (oral), ESTABLISH-2 (IV/PO)
Non-inferiority trail design vs Linezolid
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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14. 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 14

15. 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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16. 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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17. Clinical studies show DDI advantage over linezolid
No monoamine oxidase mediated interactions
Phase 1 - Tyramine:
• Tedizolid similar to placebo. No dietary restrictions necessary
• Linezolid induces 5-fold increase in tyramine sensitivity
Phase 1 - Noradrenergic:
• Tedizolid similar to placebo. No increase in mean blood pressure
• Linezolid induces 113% increase in mean blood pressure
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18. Tedizolid showed no interactions with SSRIs
Mouse Head Twitch Study
69
13 13
Placebo Tedizolid Linezolid
(30X human exposure) (1X human exposure)
18

19. Differences between ESTABLISH-1 and 2
• IV to oral switch: minimum 1-day of IV dosing
– Slightly higher exposure for tedizolid IV (~8%)
– No differences expected in efficacy or safety
• Patient demographics
– ESTABLISH-1: 80% US; ESTABLISH-2: 50% US
• X-US patients have statistically larger lesions (ESTABLISH-1)
• Tedizolid response rate vs linezolid enhanced in larger lesions
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20. Rapid efficacy in severe cellulitis
Screen Day 3 Day 10
337cm2 0 cm2 0 cm2
20

21. High cellulitis efficacy at both FDA + EMA endpoints*
Difficult to treat deep tissue infections
Tedizolid
Linezolid 98%
91%
82%
78%
FDA Endpoint EMA Endpoint
*Clinical cure at days 17-21 21

22. Tedizolid on track toward market
• ESTABLISH-2 enrollment completion: Q4 2012
• ESTABLISH-2 top line data: H1 2013
• ABSSSI NDA filing: H2 2013
• Potential NDA approval: mid 2014*
* With Priority Review afforded by the GAIN Act
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23. Gyrase: broad spectrum antibacterial program
• Potent activity against gram negative and gram positive pathogens
• Novel chemical class, broad IP rights
• Funded through Phase 1 from 5-year $28M NIAID contract
• Expected to enter clinic 2013
• First data roll out at ICAAC (9/12): 14 posters, 1 oral presentation
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24. Strong balance sheet
Cash and Marketable Securities (9/30/12) $71M
Long-term Debt (9/30/12) $0M
Shares Outstanding (11/1/12) 39.4M
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25. 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
– De-risked asset with high efficacy & superior safety
• Bayer collaboration to generate additional clinical data
• Broad spectrum gyrase program entering clinic in 2013
• Significant potential near-term catalysts
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26. The Future of Anti-Infectives
2012 Credit Suisse Healthcare Conference
November 14, 2012
26