Idenix Pharmaceuticals Building a Leading Antiviral Franchise. Cowen & Company 27 th Annual Healthcare Conference March 13, 2007 Boston

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1 Idenix Pharmaceuticals Building a Leading Antiviral Franchise Cowen & Company 27 th Annual Healthcare Conference March 13, 2007 Boston

2 Safe Harbor This presentation includes forward-looking statements about Idenix and its business, including without limitation, statements regarding drug discovery, research and clinical development, regulatory approval processes, market opportunities and commercialization activities. These forward-looking statements are subject to risks and uncertainties that may cause actual events or results to differ materially from our current expectations. These risks and uncertainties are detailed in our filings with the Securities and Exchange Commission. All forward-looking statements speak only as of the date of this presentation and, except as required by law, we undertake no obligation to update such statements. 2 2

3 Idenix Building a Leading Antiviral Franchise Mission Alliance Discover, develop and commercialize innovative antiviral drugs addressing unmet medical needs in large and growing markets Novartis global alliance enhances commercial and financial position Products 1 U.S. approved product, a robust pipeline of HBV, HCV, and HIV antiviral candidates Global Structure More than 270 employees Financial Position Strong cash position, no debt 3 3

4 Building Critical Mass of Programs for Each Indication Indication Program Preclinical Phase I Phase II Phase III NDA / U.S. Approval HBV Tyzeka /Sebivo (telbivudine) Valtorcitabine (val-ldc) Valopicitabine (NM283) HCV Discovery Program* (nucleoside, non-nucleoside, protease inhibitor) HIV IDX * previously called NV-08 4

5 Hepatitis B

6 Market Growth Driven by Novel Antiviral Therapies Global HBV Antiviral Sales Forecast (USD millions) 1,500 2,000 Anti-virals: Lamivudine Adefovir Entecavir Telbivudine Other anti-virals Key Market Drivers Launch of more potent therapies Significant expansion of diagnosed/treated patient population Increased use of combination therapy Sources: 1. IMS 2. Decision Resources 6

7 HBV Nucleoside U.S. Market Strong Market Growth 8,000 7,000 6,000 adefovir lamivudine entecavir telbivudine total nucleoside Weekly New Rx 5,000 4,000 3,000 2,000 1,000 0 Jan-05 Mar-05 May-05 Jul-05 Sep-05 Nov-05 Jan-06 Mar-06 May-06 Jul-06 Sep-06 Nov-06 Jan-07 7 Source: IMS Weekly Oral Nucleoside Rx Data 7

8 Tyzeka /Sebivo Anticipated Approval Schedule Approved Expected decision in 2007 Filed, decisions pending 8 8

9 Clinical Data Provide Competitive Profile at Launch Comprehensive data base, including significant antiviral activity compared to lamivudine and adefovir in head-to-head clinical trials GLOBE study data provide insight into real-life clinical practice Phase III trial data are difficult to compare Different primary endpoints Different study designs GLOBE study was the only HBV registration trial prospectively designed as a true intent-to-treat analysis 9 9

10 Hepatitis B Patient Management Paradigm Early and Regular Monitoring of HBV DNA Response and Outcomes Start Treatment Drug Early Predictor of Efficacy: Rapid HBV DNA Reduction Undetectable Virus (PCR-) AT Week 24 Telbivudine GLOBE data HBeAg+ 45% HBeAg- 80% Monitor Signposts Continue Add Switch 10 10

11 TYZEKA Ongoing Phase IIIb-IV Program Continuing Data to Support Product Profile Trial Early viral kinetics vs. entecavir Combination study with pegylated interferon α-2a Lamivudine-resistant patients PROACTIV Design Telbivudine vs. entecavir for 12 weeks 40 HBeAg-positive patients 104 wks tx with telbivudine in combo w/ 52 wks pegylated interferon α-2a vs. pegylated interferon α-2a monotherapy (52 wks tx) vs. telbivudine monotherapy (104 wks tx) 300 HBeAg-positive patients Telbivudine plus adefovir vs. adefovir monotherapy in lamivudine-resistant patients 150 patients 96-week study Telbivudine plus adefovir vs. telbivudine plus tenofovir vs. continued adefovir treatment in patients who are sub-optimal responders after >6 months of adefovir monotherapy 180 HBeAg-positive and negative patients Two-year study (primary endpoint at 24 weeks) Status Ongoing Ongoing Planned Planned 11 11

12 Goal: Position Tyzeka as First-line Treatment of Choice Approved and commercially available in more than 10 countries Approvals and launches anticipated in major markets in 2007 Tyzeka offers a good chance of achieving PCR negativity at week 24 to patients and physicians Only HBV drug approved in U.S. with pregnancy category B Tyzeka: safety, efficacy and convenience for chronic HBV patients 12 12

13 Hepatitis C

14 The Future of HCV Therapy Small Molecules will be Combined as a Cocktail to Improve SVR Rates Valopicitabine is a first-in-class nucleoside polymerase inhibitor Goal is to develop a cocktail of agents to cure the majority of HCV genotype-1 patients Protease Inhibitor Nucleoside Polymerase Inhibitor SOC: Peg + RBV Non-nucleoside Polymerase Inhibitor 14 14

15 Our Perspective on HCV Treatment Paradigm and Market Potential As Outcomes Improve the Market will Expand Annual Global Sales ($MM) Global HCV Market Sustained Viral Response Rate Interferon 24 Weeks 12% Interferon 48 Weeks 20% Interferon + RBV 33-36% Peg + RBV 42-46% Triple Combo ~65% Multiple Drug Cocktail 85%+ 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% SVR Rate (Genotype 1) 0 0% Sources: Company estimates. Schering-Plough Quarterly Reports, Hoffman La Roche Quarterly Reports, InterMune Quarterly Reports Credit Suisse First Boston: Hepatitis C Market-Competition Intensifies, March 2003 Pockros, P.J. Developments in the treatment of chronic hepatitis C. Expert Opinion on Investigational Drugs 11(4) , E E E 15

16 Valopicitabine (NM283) Clinical Development Plan First-in-Class Nucleoside Polymerase Inhibitor Ongoing Phase IIb treatment-naïve study Phase IIb treatment-refractory study Drug-drug interaction study 117 treatment-naïve patients, 3 arms: 200 mg/d NM283 + peg 200 mg/d NM283 + peg + weight-based dosing of RBV placebo + peg + weight-based dosing of RBV 2007 Projected Gain additional safety and efficacy data from ongoing trials Define optimal dosing regimen Meet with FDA to discuss registration trial Initiate clinical trials of investigational drug combinations Valopicitabine is an investigational compound for the treatment of hepatitis C that is currently being evaluated in ongoing clinical trials. The most commonly occurring adverse events are gastrointestinal side effects

17 Absolute HCV RNA to Week 36 Valopicitabine Phase IIb Treatment-Naïve Study peg-ifnα initiated arms A-D NM283 initiated in arm A TaqMan LLOD <20 IU/mL Group Wk12 Wk24 Wk36 A (800mg) 59% 62% 68% B (200mg) 44% 68% 68% C+D+E (800mg) 55% 58% 58% Mean log 10 Absolute HCV RNA (IU/mL) Valopicitabine dose reduction Amplicor LLOQ (<600 IU/mL) TaqMan LLOD (<20 IU/mL) Week 17

18 Comprehensive HCV Discovery Program Goal: Expand Pipeline with One Drug in Each Class HCV Discovery Program Complementary Next-Generation Once-a-Day Candidates Building Critical Mass in HCV Drug Development Organic Discovery & Collaborative Research Nucleoside Polymerase Inhibitors Target IND 2007 Non-nucleoside Polymerase Inhibitors Target IND 2008 Protease Inhibitors Target IND

19 Building Critical Mass in HCV Drug Development HCV pipeline is rapidly expanding through organic discovery and collaborative research and development Focused on discovering next-generation drug candidate in each of the major classes of small molecules A cocktail of oral, once-a-day small molecules will be used in combination to cure the majority of HCV genotype 1 patients Exploring the combination of antiviral agents (NM283 & SCH503034) Our goal is to ensure that NM283, if approved, is part of whichever cocktail emerges as the next standard of care, which will vary by patient population 19 19

20 HIV

21 Profile of NNRTI for HIV Selected IDX-899 to Advance in Development Preclinical data suggests that both candidates IDX-899 and IDX-989 may offer an enhanced resistance threshold with favorable pharmacokinetic and safety profiles Based on its overall profile, we have selected IDX-899 to advance into clinical testing, and will keep IDX-989 as backup Potential for oral, once-a-day dosing Negative genotoxicity Potent activity against wild type and mutant forms of HIV in vitro No toxicities in two animal species even at high doses (equivalent to 10g/day in man) Phase Ib/IIa studies planned for this year 21 21

22 Corporate

23 Idenix/Novartis Strategic Alliance Landmark Biotech/Pharma Deal Established in May 2003 Equity purchase: Novartis currently holds 56% of Idenix License Agreement First right of refusal to Idenix pipeline Terms for any licensed product Novartis fully funds development from point of license forward License fees, regulatory milestones and sales milestones Co-promotion and profit split in U.S. and 5 major E.U. countries for all licensed products Licensed HBV program (telbivudine and valtorcitabine) in May 2003 $110 million in potential licensing fees and regulatory milestone payments Licensed valopicitabine (NM283) for HCV in March 2006 $550 in potential license fees and regulatory milestone payments 23 23

24 Cash Flow Summary $ in millions 12/31/05 Cash Balance, incl. marketable sec. 1Q 06 Cash Flow Valopicitabine license fee 3/31/06 Cash Balance, incl. marketable sec. 2Q 06 Cash Flow 6/30/06 Cash Balance, incl. marketable sec. 3Q 06 Cash Flow 9/30/06 Cash Balance, incl. marketable sec. 4Q 06 Cash Flow ($22.3) $25.0 ($18.1) ($17.1) ($23.3) $242.2 $244.8 $226.7 $ /31/06 Cash Balance, incl. marketable sec. $186.4 Expect to end 2007 with between $100 million and $110 million of cash, cash equivalents and marketable securities 24 24

25 2007 Momentum is Building HBV Anticipated approval and launch of SEBIVO in Europe Anticipated approval and launch of SEBIVO in Asia Phase III go/no-go decision for valtorcitabine HCV Final data from drug-drug interaction study Final data from ongoing phase IIb studies of valopicitabine Target IND for second-generation nucleoside polymerase inhibitor HIV File traditional IND Phase Ib/IIa dose-ranging study of selected compound 25 25

26 Idenix Pharmaceuticals: Building a Leading Antiviral Franchise Investor Contact: Amy Sullivan Vice President, Corporate Communications investor@idenix.com

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