1. Best-in-Class Anti-Infectives

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.
Trius has filed a registration statement (including a base prospectus) with the United States Securities and Exchange Commission for
the offering to which this communication relates. Before you invest, you should carefully review the prospectus supplement and the
accompanying prospectus, together with the information incorporated by reference therein, as well as any free writing prospectus that
Trius or the underwriters provide you in connection with the offering, for more information about Trius and the offering. Trius files annual
reports, quarterly reports and other documents with the Securities and Exchange Commission. You should read the documents we
have filed with the Securities and Exchange Commission for more complete information about Trius. You may get these documents for
free by visiting EDGAR on the Securities and Exchange Commission web site at www.sec.gov, or by visiting the Trius Therapeutics’
website at www.triusrx.com.
2

3. Record of Successful Execution
All Efficacy and Safety Objectives Achieved
• Unsurpassed efficacy & improved safety with shorter
112 Trial Successful course of therapy and better convenience
• Successful efficacy and safety results triggered $5M
milestone payment from Bayer
Enrollment on track
113 Trial Enrolling • Top line data expected early 2013
Asia-Pacific/Emerging Markets
• A strong partner with comprehensive development
Bayer Deal and commercial infrastructure in Asia
• Accelerates development in skin and lung infections
globally
Funded through Phase 1 by $28M NIAID Contract
GyrB Gram Program • Broad spectrum potency goals achieved
• IND enabling studies underway
3

4. Trius Pipeline
Tedizolid Development Program Matched with Market Opportunity
Product and Dosage Discovery /
Target Indications Form Pre-Clinical Phase 1 Phase 2 Phase 3
Oral
Tedizolid Phosphate
ABSSSI IV/
Oral
Tedizolid Phosphate IV/
Oral
HAP/VAP
Tedizolid Phosphate IV/
Oral
Bacteremia
GyrB/ParE
Drugs for Gram-Negative IV
Infections
Marine Natural Products
Drugs for Gram-Positive & IV
Gram-Negative Infections
4

5. Gram Positive Market Has Doubled in Value
Market has grown to over $2.5B globally ($1.5B in USA) with declining Vancomycin
susceptibility contributing to growth of branded agents
U.S. Sales 2005 – $700MM U.S. Sales 2011 - $1.68B
Vibativ
(Telavancin)
Vancomycin $10M*
Tygacil
(Tigecycline) Tygacil (Generic)
$10MM Vancomycin $186MM*
(Tigecycline)
(Generic) $148MM
$137MM
Cubicin Zyvox
(Daptomycin)
(Linezolid)
$114MM Zyvox
$640MM
(Linezolid) Cubicin
$437MM (Daptomycin)
$699MM
18% CAGR in Branded Sales from 2005-2011
Each market share point for a branded agent is worth $50MM
Source: Company Reports / IMS-National Sales Perspectives; *=Estimate 5

6. Tedizolid Combining the Strength of Current Products
Generic
Attribute Linezolid Vancomycin Daptomycin Tedizolid
IV/Oral
In-Vivo Bactericidal
Active in Lung
Infections
Once Daily Treatment
Short Course of
Therapy
6

7. Market Research Indicates Formulary Acceptance
For Core Indications
Priced at Parity Per Course of Priced at Significant Premium Per
Therapy to Zyvox Course of Therapy to Zyvox
cSSSi
cSSSi
60% 40% 30% 40% 30%
Pneumonia
Pneumonia
(HAP/VAP)
(HAP/VAP)
80% 20% 50% 20% 30%
Endocarditis /
Endocarditis /
Bacteremia
Bacteremia
50% 40% 10% 30% 40% 30%
0% 20% 40% 60% 80% 100% 0% 20% 40% 60% 80% 100%
Very Likely Moderately Likely Not At All Likely Very Likely Moderately Likely Not At All Likely
Based upon the response of 10 HMO/PBMS and 10 Formulary Directors
PG Decision Metrics market research of 10 Formulary Directors & 10 HMO/PBMs. Commissioned by Trius in 2009 7

8. …and Good Placement of the Oral Formulation
in the Outpatient Setting
Priced at Parity Per Course of Priced at Significant Premium Per
Therapy to Zyvox Course of Therapy to Zyvox
100% 100%
90% 90%
90% 90%
80% 80%
70% 70%
60% 60%
50% 50%
40% 40%
30% 30%
20% 20%
10% 10%
10% 10%
0% 0%
0% 0%
Tier 1 Tier 2 Tier 3 Tier 1 Tier 2 Tier 3
Based upon the response of 10 HMO/PBMS
PG Decision Metrics market research of 10 HMO/PBMs. Commissioned by Trius in 2009. 8

9. Tedizolid Phosphate Phase 3 Study Design:
Oral (112) and IV/Oral (113) Trials Under SPA
FDA and EMA Endpoints for Global Registration
Safety Analyses
Patient
Screening
6-Days Tedizolid QD 4-Days Placebo
Post Treatment
667
Evaluations
Randomization 10-Days Linezolid BID
Baseline
FDA EMA EMA
FDA Primary Endpoint Secondary Primary Secondary
48-72 hrs from Baseline Endpoints Endpoint at Endpoint
at EOT PTE LFU
9

10. Primary Outcome: All Current and Contemplated Trial 112
Primary Endpoints Achieved in Pre-Specified Analyses
Primary Outcome at 48-72 hour visit Treatment
Lesion Criteria Tedizolid Linezolid
Fever Criteria (200 mg QD 6 days) (600 mg BID 10 days)
112 SPA Primary Endpoint Temperature measurements
No increase in lesion area required within 24 hrs of 79.5% 79.4%
from baseline* 48-72 hr visit*
FNIH recommended to FDA to exclude temperature as a component of the primary endpoint
and to assess a >20% reduction in lesion size at 48 to 72 hours.
Under these pre-specified analysis tedizold shows additional numerical separation from linezolid
No increase in lesion area
from baseline Temperature excluded** 87.0% 85.4%
FNIH Primary Endpoint
≥ 20% reduction of lesion Temperature excluded** 78.0% 76.1%
are from baseline**
* Primary endpoint as agreed to under Study 112 and 113 SPA
** FNIH recommendations to FDA: ABSSSI Docket ID: FDA--2010--D--0433
10

11. Secondary Outcomes: Tedizolid Demonstrates
Comparable Efficacy with Shorter Course of Therapy
Secondary Outcome at EOT or PTE Treatment
Secondary Outcome Tedizolid Linezolid
Criteria (200 mg QD 6 days) (600 mg BID 10 days)
112 SPA 69.3% (ITT) 71.9% (ITT)
Early clinical failures carried
Clinical Response at EOT*
forward to EOT*
(Day 11) 80.2% (CE) 81.1% (CE)
In August 2010 draft guidance the FDA adopted changes to the secondary outcomes of clinical response
at the end of therapy (EOT). These were prospectively measured in Study 112 sensitivity analyses and
are captured in the Study 113 SPA.
80.7% (ITT) 80.9% (ITT)
Clinical Response at EOT* Early clinical failures not carried
(Day 11) forward to EOT**
87.5% (CE) 87.1% (CE)
Early clinical failures not carried 87.0% (ITT) 87.8% (ITT)
113 SPA
forward to EOT** and
Clinical Response at EOT* presence/absence of patient
(Day 11) reported pain at EOT excluded*/** 94.5% (CE) 95.1% (CE)
* Primary and secondary endpoints as agreed to under Study 112 SPA
** Consistent with FDA draft ABSSSI Guidance for Industry (August 2010)
11

12. Tedizolid was Well Tolerated with a Favorable AE
Profile Compared to Linezolid
Tedizolid had a numerically lower rate of drug-related treatment emergent adverse events
(TEAE) and a statistically significant lower number of gastrointestinal adverse events
Tedizolid Linezolid
Adverse Event
(200 mg QD 6 Days) (600 mg BID 10 Days)
Any Treatment Emergent
40.8% 43.3%
Adverse Event (TEAE)
Any Drug Related TEAE 24.2% 31.0%
Gastrointestinal
16.3%** 25.4%
Disorders*
* Gastrointestinal AEs include: Diarrhea, Nausea, Vomiting and Dyspepsia
** Statistically significant (p=0.004).
No Unexpected Safety Signals
• Liver enzymes/function tests
• QTc
12

13. Hematology: Tedizolid Had Significantly Lower Impact
on Platelets than Linezolid
Percent of Patients with Value below the
Lower Limit of Normal (LLN)
Tedizolid Linezolid
Hematology Parameter
(200mg QD 6 days) (600mg BID 10 days)
Platelets*
9.2% 14.9%
Below LLN
Platelets – Substantially
Abnormal Value 2.3% 4.9%
(<75% LLN)
* Statistically significant (p=0.038)
13

14. Phase 3 Trial Summary
£ Study 112 design and outcomes are consistent with both FDA and EMA
regulatory requirements
£ All efficacy and safety objectives of Study 112 were successfully
achieved
– Efficacy: All primary and secondary trial endpoints met with a once-daily
short course of therapy
– Safety: statistically significant lower incidence in key tolerability and
safety parameters
– Successful results triggered $5M milestone payment from Bayer
£ Results align with surveyed physician and payer preferences for fast
acting drugs with improved tolerability and safety*
* PG Decision Metrics market research of 10 Formulary Directors & 10 HMO/PBMs. Commissioned by Trius in 2009
AMR – Hospital Insight Series, US Data, August 2011
Hawk Partners - Target Product Profile Research with 29 US Physicians. Commissioned by Trius, Sept 2011
14

15. Bayer Strategic Collaboration for Asia-Pacific and
Emerging Markets
Exclusive license to develop and
Retains rights to Obtains key asset for
commercialize tedizolid in Asia,
largest commercial largest therapeutic
Africa, Latin America and the Middle area in licensed
opportunity East (ex-Korea) territory
Trius leads
Responsible for all
development of global $25M upfront independent regional
clinical studies development
$69M in development, regulatory
Enables early and commercial milestones Responsible for all
execution of ex-U.S. marketing activities in
commercial strategy its territory
25% of the future development costs
in ABSSSI and pneumonia
Double digit royalties
15

16. Gyrase-B Program: Novel Class of Broad Spectrum Antibiotics
£ Funded through Phase 1 by $28MM NIAID Contract
£ Lead molecules have potent activity against gram-negative and
gram-positive bacterial pathogens
£ including MRSA, ESBL strains, Pseudomonas, Acinetobacter & Klebsiella
(including NDM1)
£ Efficacy demonstrated in multiple animal models
£ Lung, urinary tract, thigh, septicemia
£ Clean nonclinical toxicity and no CYP450 interactions
£ Including dog CV telemetry study up to 10x efficacious drug exposure.
No effect on all CV parameters (Qtc, HR, BP etc.).
£ Clinical studies expected to start 2012
16

17. Evolution of MICs in Lead Series Against Gram Negative
and Gram Positive Pathogens
Antibacterial Potency MIC (µg/mL)
Adverse Event 1491 1710 1722 1852
S. aureus 0.008 0.008 0.008 0.008
S. pneumoniae 0.008 0.008 0.008 0.004
E. coli (wt) 0.25 0.13 0.25 0.13
K. pneumoniae (MDR) 2 2 2 1
A. baumannii 0.50 0.25 0.50 0.25
P. aeruginosa (wt) 4 2 1 0.50
Gram + Gram —
17

18. MIC90 of GyrB/ParE Development Candidate vs
Comparators against Gram-Positive Pathogens
MIC90
of
TR-­‐1852
vs.
G+
isolates
>16
16
>4
>4
>4
14
12
8
MIC90
(µg/ml)
4
10
4
2
8
ciprofloxacin
6
0.25
1
linezolid
4
2
0.5
vancomycin
2
≤0.001
≤0.001
daptomycin
0
0.03
TR-­‐1852
Number of isolates is shown in parentheses
18

19. MIC90 of GyrB/ParE Development Candidate vs
Comparators against Gram-Negative Pathogens
**
*
***
*
Includes
ESBL
isolates
**
includes
MDR,
ESBL
isolates
***
includes
ESBL,
NDM-­‐1,
KPC-­‐2,
KPC-­‐3,
and
randomly
selected
isolates
19

20. P. aeruginosa MIC90 Results for TR-1852 (50 strains)
P.
aeruginosa
MIC90
panel
100
MIC90 = 1 µg/mL
90
80
70
%
strains
cumulaKve
60
1852
Cefepime
50
Cipro
Gent
40
Imipenem
30
20
10
0
0.06
0.125
0.25
0.5
1
2
4
8
16
32
64
128
MIC value µg/mL
20

21. E. coli Mouse Urinary Tract Infection Model
Mouse Ascending UTI Model − E. coli
Drugs Dosed IV 10 mg/kg/day
7
Bladder
Average Log10 CFU/g Tissue
6
Kidney
5
4
3
2
1
0
C 1852 Levo C 1852 Levo
21

22. Safety Summary: Clean In-Vitro & In-Vivo to Date
£ No CYP450 inhibition – low drug-drug interaction potential
£ No Relevant Off-Target Enzyme Activities – bacterial selective
£ No Genotoxicity Signals (human cell line)
£ Clean in Dog Cardiovascular Study – all parameters including QTc
£ Single Dose MTD in Mice & Rats >100 mg/kg
£ Rat Chronic 14 Day Dose NOAEL ~50 mg/kg*
– Therapeutic Margin Estimate (~13x)**
*Pending histopathology, based on gross necropsy, blood biochemistry & hematology
**AUC @ NOAEL dose/AUC @ efficacious dose
22

23. Capitalization
Cash & Equivalents (at 9-30-11) $70MM
Long Term Debt (at 9-30-11) $0MM
Federal Contracts Awarded $60MM
Shares Outstanding 38.6MM
Market Capitalization (at 2-10-12) $211MM
Cash Runway* Q3 2013
* Assumes initiation of global HAP study in 2013 and no additional partnerships
23

24. Upcoming Goals
§ Potential European partnership
§ Regulatory agreement enabling initiation of Phase 3 pneumonia study
§ IND filing for Gyrase clinical candidate
§ Completion of enrollment for 113 Phase 3 ABSSSI trial
24

25. Best-in-Class Anti-Infectives