1 Michael V. Novinski President and Chief Executive Officer November 6, 2008 Third Quarter 2008 Earnings Conference Call

2 Safe Harbor Safe Harbor Statement Regarding Forward-Looking Statements The statements in this release and oral statements made by representatives of Emisphere relating to matters that are not historical facts (including without limitation those regarding the timing or potential outcomes of research collaborations or clinical trials, any market that might develop for any of Emisphere's product candidates and the sufficiency of Emisphere's cash and other capital resources) are forward-looking statements that involve risks and uncertainties, including, but not limited to, the likelihood that future research will prove successful, the likelihood that any product in the research pipeline will receive regulatory approval in the United States or abroad, the ability of Emisphere and/or its partners to develop, manufacture and commercialize products using Emisphere's drug delivery technology, Emisphere's ability to fund such efforts with or without partners, and other risks and uncertainties detailed in Emisphere's filings with the Securities and Exchange Commission, including those factors discussed under the caption "Risk Factors" in Emisphere's Annual Report on Form 10-K (file no ) filed on March 13, 2008 and our Quarterly Report on Form 10-Q for the quarter ended June 30, 2008, filed on August 11, 2008.

Agenda  Introductory Remarks  Financials  Eligen ® B12 Commercialization  Partnerships  Cash Position  Questions

4 Introductory Remarks

5 Eligen ® B12 – Clinical Strategy  Human clinical trials of B12 formulations in healthy volunteers demonstrate Eligen ® B12 provides new mechanism for B12 delivery Eligen ® B12 significantly enhances B12 absorption  C max (greater than tenfold compared to commercial)  T max (reduced by more than 90%)  Clinical investigation of Eligen ® B12 therapeutic efficacy in target populations set for fourth quarter One study in B12 deficient subjects to be initiated in 2008 Additional studies scheduled for 2009

6  Clinical strategy to support higher and lower dose  Regulatory strategy GRAS  Valuation in process with physicians and consumers  Exploring various market opportunities with a potential market entry in late 2009 Eligen ® B12 – Commercial Application

Novartis and Salmon Calcitonin  Recruitment completed for two Phase III studies by Novartis exploring effects of Eligen ® and Salmon Calcitonin in osteoarthritis and osteoporosis Phase III study exploring safety and efficacy of Oral Salmon Calcitonin in the treatment of vertebral fractures in postmenopausal women aged in North and South America, Europe and Asia Phase III study exploring the safety and efficacy of Oral Salmon Calcitonin to treat patients with knee osteoarthritis in patients aged mainly in Europe; estimated completion in 2010  This study will be used to support the filing with health authorities worldwide  A second study, designed to meet FDA requirements for U.S. registration, was initiated in October 2008 Partnerships

8 Novartis and Salmon Calcitonin  Publication of study of Oral Salmon Calcitonin using Eligen ® Technology taken minutes before meals with 50ml of water resulted in improved absorption and efficacy compared to nasal formulation Partnerships

GLP-1 Study Findings  Independent study published showed that GLP-1 and PYY3-36 can be delivered orally in humans safely and efficiently Conducted at University Hospital in Basel, Switzerland, by Christoph Beglinger, M.D.

10 Cash Position  Current cash sufficient for next six months  Negotiations on partnerships continue

11 Stock Performance  Currently undervalued  Share price affected by overall market conditions  Continued exposure to financial community Rodman & Renshaw Conference – November NYSSA Conference – December Ongoing one-on-one investor meetings and calls

12 Summary  Unique technology selected by key pharmaceutical companies  Solution-based alternative for many pharmaceutical development issues  Highly adaptive to various therapeutic fields  Carriers themselves are not pharmacologically active  Not limited to prescription drug products (B12, nutrients, other vitamins, etc)  Two Phase III programs Osteoarthritis Osteoporosis  Newly established leadership position for oral therapy Type II Diabetes  Potential commercial product late-2009

Q&A