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The Future of Anti-Infectives

September 5, 2012

Baird Healthcare Conference

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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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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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Pre-clinicalPre-clinical Phase 1Phase 1 Phase 2Phase 2 Phase 3Phase 3

Tedizolid Phosphate

Oral

IV/Oral

HAP/VAP IV

Bacteremia IV/Oral

GyrB/ParE

Gram- Infections IV

ABSSSI

Trius pipeline

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Strong growth in MRSA* treatment days

Source: AMR (United States market) *methicillin-resistant Staphylococcus aureus

Total hospital treatment days in US

(Vancomycin, Linezolid and Daptomycin)

2005 2006 2007 2008 2009 2010

16.7M

21.1M 21.0M 22.2M

24.0M 25.8M

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Increasing resistance to vancomycin

Resistance of MRSA against Vancomycin

Source: Theravance Company Report, April 2010 & AMR (United States market).

AMR - Hospital Insight Series, US Data, August 2011

2.8% 3.3%

3.8%

9.2%

11.1%

2005 2006 2007 2008 2009

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Physician attitude on vancomycin is changing

Source: AMR - Hospital Insight Series, US Data, August 2011

51% 39%

9%

6% 8%

48%

CubicinZyvoxVancomycin

Percent of physicians reporting decreased or increased perscriptions

Less

M

ore

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Tedizolid: highly differentiated oxazolidinone

Tedizolid Linezolid (Zyvox)

Week 1 Week 2 Week 1 Week 2

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Strong product profile

Attribute Linezolid Vancomycin Daptomycin Tedizolid

IV/Oral

In-Vivo Bactericidal

Active in Lung

Infections

Once Daily

Treatment

Short Course of

Therapy

Generic

X

X

X

X

X

X X

X

X

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Phase 3 trial design: ESTABLISH-1 (oral), ESTABLISH-2 (IV/PO)

2o

EMA

1o

EMA

Tedizolid

Linezolid

1x 200mg

2x 600mg

n=667

1o

FDA

2o

FDA

Placebo

Post-Treatment Evaluations

END-POINTS FOR GLOBAL REGISTRATION

Safety Analysis

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1o endpoint achieved: current & expected guidance

Lesion Criteria (Area)

No increase from baseline

Fever Criteria (Temperature)

Measurements required

Lesion Criteria (Area)

≥20% reduction from baseline

Fever Criteria (Temperature)

Excluded*

79.5%

78.0%

79.4%

76.1%

Current Guidelines* Expected Guidelines**

Tedizolid

Linezolid

* Primary endpoint as agreed to under Study 112 and 113 SPA

** FNIH recommendations to FDA: ABSSSI Docket ID: FDA-2010-D-0433

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Significantly lower impact on platelets

2.3% 4.9%

9.2%*

14.9%*

TedizolidLinezolid

75% - 100% LLN (112-150K/μL)

<75% LLN (<112K/μL)

* Statistically significant difference

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Phase 3: lower rates of adverse events

TEAE = Treatment Emergent Adverse Event

Gastrointestinal AEs incl. diarrhea, nausea, vomiting & dyspepsia

* Statistically significant difference: p = 0.004

43.3%

31.0%

25.4%

40.8%

24.2%

16.3%*

Any TEAE Drug-Related TEAE GI Disorder

Linezolid Tedizolid

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Tedizolid on track toward market

* With Priority Review afforded by the GAIN Act

• 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*

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Upcoming catalysts and milestones

ProgramEvent Timing

Present Abstracts at ICAAC Sep 2012

Top-line Data - 2nd Phase 3 in ABSSSI H1 2013

File NDA H2 2013

Potential European Partnership 2012/13

Potential U.S. Launch 2014

Present Abstracts at ICAAC Sep 2012

File IND/Initiate Phase 1 2013

Tediz

olid

Gyra

se

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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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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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The Future of Anti-Infectives

September 5, 2012

Baird Healthcare Conference