Nasdaq: IDRA

1. Lou Arcudi, Chief Financial Officer • Noble Financial Capital Market’s Seventh Annual Equity Conference Clinical Pipeline + Discovery Platform Translational Research Nasdaq: IDRA May 2011

2. Safe Harbor Statement Any statements that we may make in this presentation about future expectations, plans and prospects for the Company constitute forward-looking statements for purposes of the safe harbor provisions under The Private Securities Litigation Reform Act of 1995. Actual results may differ materially from those indicated by these forward-looking statements as a result of various important factors, including risks as to whether results obtained in preclinical studies or early clinical trials will be indicative of results obtained in future studies or trials; whether products based on Idera’s technology will advance through the clinical trial process and receive regulatory approval on a timely basis or at all; whether, if such products receive approval, they will be successfully distributed and marketed; whether the Company’s collaborations will result in successful product development and in the Company receiving payments thereunder; whether the patent and patent applications owned or licensed by Idera will protect the Company's technology and prevent others from infringing it; whether Idera's cash resources will be sufficient to fund product development and other operations; and such other important factors as are set forth under the caption "Risk Factors" in Idera’s Quarterly Report on Form 10Q for the three months ended March 31, 2011. Idera disclaims any intention or obligation to update any forward-looking statements.

3. Idera: Clinical Stage Development Company • Diverse clinical-stage pipeline of proprietary and partnered drug candidates targeting Toll-like receptors (TLRs) • Clinical data validating scientific rationale in Oncology, Chronic Hepatitis C Virus Infection, and Autoimmune Diseases • In 2011, multiple clinical programs in Phase 2 • Entire development portfolio generated by Idera’schemistry-based TLR drug discovery capability • Strong patent position, over 500 patents in portfolio

4. Idera’s Pipeline of Candidates COLLABORATION WITH COLLABORATION WITH

5. Idera’s TLR-Targeted Candidates TLR Signaling Chemistry Drug Candidates Endosome Cytoplasm IMO-2055 IMO-2125 IMO-3100 IMO-2134 IMO-4200 IMO-5001 IMO-2311 IMO-2314 IMO-2295 Nucleus NK Cells pDCs B cells Macrophages/ Monocytes mDCs

6. IMO-2055: for the Treatment of Cancer • IMO-2055, a TLR9 agonist, induces innate and adaptive immune responses • IMO-2055 shows anticancer activity in multiple preclinical tumor models • IMO-2055 potentiates anticancer activity of Erbitux® in preclinical tumor models • Mechanism of action of IMO-2055 provides a rationale for targeted immunotherapy of cancer IMO-2055 B cells pDCs Th1-type immune responses NK Cell Activation Antitumor Activity Erbitux® Enhanced antitumor activity

7. IMO-2055: Collaboration with Merck KGaA COLLABORATION WITH • Entered into collaboration with Merck KGaA in December 2007 for discovery and development of TLR9 agonists for cancer treatment • Business terms • $40M upfront payments received • Total potential milestones remaining €255M • Commercialization royalties: mid-single digit escalating to low-double digit • R&D costs covered by Merck KGaA • Milestone Payments Received • $12M associated with initiation of three trials • Merck KGaA is conducting clinical trials of IMO-2055 (EMD 1201081) in combination with other cancer therapy agents including a Phase 2 clinical trial in head and neck cancer

8. IMO-2125: A Novel Immune Modulator for Treatment of Hepatitis C Virus Infection • IMO-2125 induces TLR9-mediated immune responses including: • Endogenous antiviral cytokines • IFN-α, IP-10, 2’,5’-OAS, etc. • Cellular activation: • NK cells, monocytes, neutrophils • Enhances Th1-type immune response • IMO-2125 provides rationale for novel immune modulator as an alternative to recombinant interferon IMO-2125 B cells pDCs Th1-type immune responses Type I Interferons Cellular Activation

9. IMO-2125: Phase 1 Clinical Trials in Null-Responder and Treatment-Naïve HCV Patients • Two Phase 1 trials completed in 118 patients, four-week treatment periods • Null-responder patients, IMO-2125 monotherapy • 58 patients, 6 dose regimens • Treatment-naïve patients, IMO-2125 plus ribavirin • 60 patients, 4 dose regimens • Comparative arm: Pegasys® plus ribavirin • Study endpoints • Safety and tolerability • Antiviral activity

10. IMO-2125: Safety Profile • IMO-2125 was well-tolerated in approximately 96 patients • No discontinuations, no treatment-related SAEs • Most common AEs in patients receiving IMO-2125 were • Mild-moderate injection site reactions (e.g., erythema, induration, tenderness) • Mild-moderate flu-like symptoms (e.g., fever, chills, myalgias) • Treatment-naïve patients receiving IMO-2125, compared to Pegasys®, experienced: • Shorter duration of flu-like symptoms • Limited neutropenia and thrombocytopenia

11. IMO-2125: Antiviral Activity • IMO-2125 induced a broad array of antiviral cytokines and chemokines, including interferon-alpha in both patient populations • At all dose levels IMO-2125 induced declines in viral levels at 48 hours after the first dose in treatment-naïve patients • IMO-2125 at all dose levels produced substantial viral load reductions after four weeks of treatment in both patient populations • IMO-2125 treatment led to AST and ALT levels within normal limits by the end of the fourth week of treatment in treatment-naïve patients

12. IMO-2125: Planned Phase 2 Clinical Trial • Patient Population and Treatment • Treatment-naïve HCV-infected patients • 12-week treatment period • Treatment with IMO-2125 + ribavirin • Control arm treated with Pegasys®+ribavirin • Study endpoints: • Detailed monitoring of safety and tolerability • Antiviral activity • Path forward to be determined after evaluation of data from nonclinical toxicology studies, which we expect will be available in 2H 2011 • Planned Phase 2 trial designed to guide clinical development of • IMO-2125 for use in combination with Direct-Acting Antiviral agents

13. IMO-3100: Novel Approach for Treating Autoimmune Diseases • TLR7 and TLR9 are implicated in autoimmune and inflammatory diseases • IMO-3100 inhibited immune responses mediated through TLR7 or TLR9 • IMO-3100 activity confirmed in several preclinical models of autoimmune diseases including: lupus, psoriasis, rheumatoid arthritis and hyperlipidemia • IMO-3100 inhibits induction of multiple cytokines and provides a novel approach for the treatment of autoimmune diseases Immune complexes act as Endogenous Ligands IMO-3100 B cells pDCs X X X X IFN-α, IP-10, IL-12, IL-6, TNF-α, IL-1β, Anti-RNP, Anti-ds DNA IFN-α, IP-10, IL-12, IL-6, TNF-α, IL-1β, Anti-RNP, Anti-ds DNA

14. IMO-3100: Safety and Mechanism of Action in Clinical Studies • Two Phase 1 clinical trials completed in 60 healthy subjects • Single-dose study • 36 healthy subjects, 5 dose levels, placebo controlled • Multiple-dose study for four weeks • 24 healthy subjects, two dose cohorts, placebo controlled • Study endpoints: • Safety • IMO-3100 well tolerated at all dose levels • Mechanism of action • Engagement of TLR7 & TLR9 confirmed in MO-3100-treated subjects through suppression of TNF-α, IL1β, IL-6, IFN-α and other cytokines

15. IMO-3100: Planning for Phase 2 Trial • Anticipated completion of ongoing nonclinical safety studies 1H 2011 • Submission of Phase 2 protocol expected 3Q 2011 • Initiation of Phase 2 anticipated by year-end 2011 • Study design anticipated to establish safety and activity of IMO-3100 over 12 weeks of treatment in a selected autoimmune disease indication • IMO-3100 inhibits induction of multiple cytokines including TNF-α, IL-6, IL-1β, IP-10 and INF-α and provides • a novel approach for the treatment of autoimmune diseases

16. Pipeline of Clinical and Preclinical Candidates • Clinical Candidate: IMO-2134 • TLR9 agonist for the treatment of respiratory diseases • Phase 1 trial conducted in healthy subjects by Novartis • Idera regained rights to this program from Novartis in 2010 • Lead Candidate: IMO-4200 • Dual TLR7 and 8 agonist for the treatment of hematological malignancies • In preclinical lymphoma models, antitumor activity and potentiation of activity of Rituxan® and Velcade® • Novel Discoveries: TLR3 agonist compounds • Use as vaccine adjuvants being studied in infectious diseases and other indications

17. TLR Agonists: For Use as Vaccine Adjuvants • Entered into collaboration with Merck & Co. in December 2006 for use of agonist of TLR7, 8 and 9 as vaccine adjuvants in the field of cancer, infectious diseases, and Alzheimer’s disease. • Business terms • $30M upfront payment • Up to $425M potential milestone payments depending on vaccines and agonists employed • Commercialization royalties: mid to upper single digit • R&D costs covered by Merck • Ongoing research • Multiple scientific presentations by Merck on immunogenicity and adjuvant activity of TLR agonist in preclinical models

18. Novel Gene-silencing Oligonucleotide Technology • Gene-silencing oligonucleotides (GSOs) are novel single-stranded DNA and RNA structures • In vitro and in vivo data demonstrate that GSOs: • Inhibit gene expression with 19-mer and 21-mer having most potent activity • Engage a similar cellular mechanism as siRNAs • Achieve systemic delivery without need for enhancement technology • Provides new platform for target validation and discovery of novel drug candidates • Next steps: conduct studies of GSOs targeted to mRNA and miRNA GSOs may overcome significant obstacles of antisense and siRNAtechnologies including stability, delivery and specificity

19. Financial Highlights Dollars in 000’s

20. 2011 Anticipated Milestones • Advancement of multiple clinical programs • Completion of Phase 2 of IMO-2055 in oncology • Determine path forward for IMO-2125 in HCV • Initiation of Phase 2 clinical trial of IMO-3100 in an autoimmune indication • Advancing the pipeline of candidates • Outline development strategy of IMO-2134 in respiratory diseases and IMO-4200 in hematological malignancies • Vaccine adjuvant application • Advancement of ongoing preclinical studies • Building alliances • Assets include IMO-2125, IMO-3100, IMO-4200, and agonists of TLR3, TLR7, TLR8 and TLR9, and gene-silencing oligonucleotide technology COLLABORATION WITH COLLABORATION WITH

21. Clinical Pipeline + Discovery Platform Translational Research Nasdaq: IDRA