MediciNova, Inc. 2008 Statements in this presentation that are not historical in nature constitute forward looking statements within the meaning of the safe harbor provisions of the Private Securities Litigation Reform A

New Lesions at Month 2 72 64 56 # Patients w. 1 PBH (% of Pts. w. New Lesions) 41 (56.9%) 33 (51.6%) 28 (50%) Mean Proportion of Lesions Evolving to PBH 0.24 0.20 0.16 Median Proportion of Lesions Evolving to PBH 0.17 0.08 0.04 Relative Risk (for Evolution to PBH) vs. placebo 0.74 0.63 p Value 0.074 0.011 New T1 gadolinium enhancing or new T2 lesions were defined as NL in the first on study MRI at month 2 Lesions that were hypointense and inactive at month 10 were PBH Relative Risk (RR) of NL evolution to PBH was analyzed using a general linear model with the error term from the Poisson distribution Reduction of Persistent Black Hole (PBH) Reduction of Persistent Black Hole (PBH) Formation, a Sign of Axonal Loss Formation, a Sign of Axonal Loss MediciNova, Inc. 2008 A.7 MN 166 was very well tolerated in Phase II study: 89% (264 of 297) of subjects completed the first 12 months of the study 82.5% (245 of 297) of subjects completed the full 24 months of the study Discontinuation due to adverse effects was infrequent (5.1% in 60 mg/day for 24 months, 2.1% in 30 mg/day for 24 months, 2.0% in placebo to 60 mg/day, 1.9% in placebo to 30 mg/day) Adverse effects were generally mild and self limiting GI adverse effects as a group and depression were the only adver se events to occur more frequently in MN 166 treated than in placebo treated subjects Tolerance to the GI side effects occurred rapidly (2 4 days) and tended to occur early in treatment whether MN 166 treatment was initiated in Year 1 or Year 2 Mild to moderate depression was reported in 8 subjects; depression is co mmon in MS patients and was reported only towards the end of the study No significant increase in adverse laboratory or ECG findings wa s observed 20 serious adverse events were reported; all were not or unlikely to be attributable to treatment No deaths occurred in the study MN 166 Overview Safety MN 166 Overview Safety MediciNova, Inc. 2008 Compound Sponsor Current Phase Safety Profile from Phase II trials MN 166 MediciNova Phase II Mild, transient GI upset FTY 720 Novartis Phase III Blood pressure Heart rate Dyspnea Liver enzymes Lymphopenia Cladribine Merck Serono Phase III Fever Nausea, Vomiting Leucopenia BG 12 Biogen Idec Phase III H/A, Nasopharyngitis GI disorders Liver enzymes Laquinimod Teva Phase III Liver enzymes Arthralgia Fibrinogen Hemoglobin Safety Comparison with Other Safety Comparison with Other Oral Agents Oral Agents A.8

Sales 2007** Compound Sponsor Side Effects $3.3 Billion Copaxone Teva Sanofi Aventis Pain, redness, swelling, itching, chest pain, weakness, infection, nausea, anxiety are most common, also heart palpitations and trouble breathing after injection $1.9 Billion Avonex Biogen Idec Depression and Flu like symptoms most common, also liver injury, severe allergic reactions, drop in red/white blood cell count $1.7 Billion Rebif Serono Pfizer Depression and Flu like symptoms most common, also liver problems, injection site problems, severe allergic reactions, trouble breathing/loss of consciousness $1.4 Billion Betaseron Bayer Lymphopenia, injection site reaction, asthenia, flu like symptoms are most common, also necrosis at injection site $343 Million Tysabri Biogen Idec Infections, depression, pneumonia, acute hypersensitivity reactions, appendicitis most common, also liver damage, PML Multiple Sclerosis Market* Multiple Sclerosis Market* *All these top selling drugs for MS are immunomodulators **Source: MedAdNews, July 2008 and BIIB annual report 2007 MediciNova, Inc. 2008 A.5 Brain volume changes are linked to axonal loss Chronic Efficacy Demonstrated: Chronic Efficacy Demonstrated: Effects on Brain Volume Effects on Brain Volume 1.20 MediciNova, Inc. 2008 A.6 Reduction of Persistent Black Hole (PBH) Formation Parameter Treatment Groups Placebo 30 mg/day 60 mg/day # Patients w.

Associate Clinical Professorship of Medicine at UCSD School of Medicine since 1985 Masatsune Okajima, CMA Masatsune Okajima, CMA VP, Head of Japanese Office 17 Daiwa Securities SMBC, Sumitomo Capital Securities, Sumitomo Bank Management Team with Global Management Team with Global Experience Experience MediciNova, Inc. 2008 25 MN 221 (Acute Exacerbations of Asthma): Proven mechanism of action Highly selective with improved safety profile vs. standard of care Positive Phase IIa efficacy data Near term milestone: CL 006 results MN 166 (Multiple Sclerosis): Both chronic and acute efficacy have been demonstrated in clinical studies completed to date MediciNova seeking a partner to advance the clinical development of MN 166 Minimized Burn Rate: Annual burn rate reduced compared to previous years as a result of focus on MN 166 and MN 221 development programs For 9/30/2008 Cash, Cash Equivalents and Marketable Securities, reference Quarterly Report on Form 10 Q filed 11/10/2008 Investment Highlights Investment Highlights MediciNova, Inc. 2008 Addendum: Addendum: Additional Data MediciNova, Inc. 2008 A.1 MN 221 Study 6 Design MN 221 Study 6 Design Randomized, modified single blind, dose escalation, placebo controlled Phase II Study in acute asthma patients in EDs Approx. 36 patients in 3 dose cohorts at 8 ED clinical sites Doses: 16 g/min x15 (240 g) 30 g/min x15 (450 g) 16 g/min x15;8 g/min x105 (1,080 g) Patients will receive Standard of Care (SOC) treatment in addition to adjunctive treatment with MN 221 or placebo Safety and efficacy (FEV1 and other) data will be summarized No inferential statistical analysis Help inform design of future, larger Phase III clinical trials MediciNova, Inc. 2008 A.2 MN 221: Safety MN 221: Safety Phase IIa Study Safety Findings: No clinically significant cardiovascular, ECG, or vital sign changes, or other safety concerns, observed at doses up to 30 micrograms/minute for 15 minutes or any time point thereafter 60 micrograms/minute infusion improved FEV1 significantly ( p 0.0001 ) without clinically significant cardiovascular, ECG or vital sign changes; however, the safety trend led us to believe that this is a possible MTD Safety Database: MN 221 has been tested in over 300 subjects in the US and Europe to date Subjects have had infusions with no clinically significant adverse events at: 16 micrograms/minute for up to 4 hours and at lower doses for up to 24 hours MediciNova, Inc. 2008 A.3 Description Efficacy (relapse rate) Current agents offer only 30 50% relapse reduction Neutralizing antibodies can diminish efficacy over time Progression (RRMS) neurodegeneration leads to permanent functional disability No approved treatment for PPMS, SPMS AEs including flu like symptoms SAEs Rare, fatal PML and heptotoxicity with Tysabri Reports of significant FTY side effects (e.g. hepatotoxicity), serious or fatal opportunistic infections, skin cancer Safety/ tolerability Injections daily up to weekly Infusions monthly Administration Increasing interest in combination therapies given incomplete efficacy with current core agents Black box on combination with Tysabri, REMS program Combination Historically, anti inflammatory agents have shown little impact on disease progression Demonstrated neuroprotection, that is, reduction in disease progression, would be groundbreaking Neuroprotection There are substantial unmet There are substantial unmet needs in MS needs in MS MediciNova, Inc. 2008 A.4 Approx.

USC, Formerly Prof. Pitt; Advisor to JAFCO, Tanabe Richard Gammans, PhD, MBA Richard Gammans, PhD, MBA Chief Development Officer 31 Incara, Indevus, BMS Shintaro Asako, CPA Shintaro Asako, CPA Chief Financial Officer 10 KPMG USA (Audit), Arthur Andersen USA Michael Kalafer, MD Michael Kalafer, MD Chief Medical Officer 25 Board Certified in Pulmonary Medicine, Critical Care Medicine and Internal Medicine.

New Lesions at Month 2 72 64 56 Total Number New Lesions in all Patients 426 338 315 Total Number of Persistent Black Holes 98 58 47 Proportion of Lesions Evolving to PBH 0.23 0.17 0.14 p Value 0.036 0.004 New T1 gadolinium enhancing or new T2 lesions were defined as NL in the first on study MRI at month 2 Lesions that were hypointense and inactive at month 10 were PBH Relative Risk (RR) of NL evolution to PBH was analyzed using a general linear model with the error term from the Poisson distribution Reduction of Persistent Black Hole Reduction of Persistent Black Hole (PBH) Formation (PBH) Formation 18 MediciNova, Inc. 2008 TREATMENT Time Period Placebo to Active ( N=100 ) Active Drug [30 mg (N=94), 60 mg (N=98)] 2 Years 21/100 (21%) 20/194 (10.4%) 19 Disability Progression is defined as a sustained increase in EDSS (increase in EDSS 1 maintained for four consecutive months) Sustained Disability Progression Sustained Disability Progression P Value: 0.026 19 MediciNova, Inc. 2008 20 Acute Efficacy Demonstrated: Acute Efficacy Demonstrated: Time to First Relapse Time to First Relapse Median 401 days Median 244 days P Value: 0.044 MediciNova, Inc. 2008 21 MN 166: NEXT STEPS MN 166: NEXT STEPS Seek Partnership for Further Development: MediciNova s strategic objective for MN 166 is to secure a partner to advance the clinical development of MN 166, and MediciNova is actively pursuing that objective MediciNova, Inc. 2008 22 Commercially Attractive Commercially Attractive Diversified Portfolio Diversified Portfolio MediciNova, Inc. 2008 23 Dual Listing: MNOV (NasdaqGM), December 2006 4875 (Osaka Hercules), February 2005 Cash, Cash Equivalents and Marketable Securities as of 6/30/08 : ~$55.8 M as of 6/30/08 Market cap as of 9/30/08: ~$27.2 M Shares outstanding: 11.9 M Key Financials Key Financials MediciNova, Inc. 2008 24 Leadership Years Experience Background Yuichi Iwaki, MD, PhD Yuichi Iwaki, MD, PhD CEO President 33 Prof.

Current Clinical Studies: Current Clinical Studies: MN 166 CL 001 MN 166 CL 001 15 MediciNova, Inc. 2008 MN 166 Effects Outcomes Related to Disease Progression in RRMS Patients Clinical and MRI Outcomes: Indicative of Potential Neuroprotective Effect: 1. Reduced Brain Volume Loss 2. Reduced Conversion of Acute Lesions to Persistent Black Holes 3. Sustained disability progression was significantly less likely (~50%) Acute Clinical Benefit: Prolong time to relapse (by 127 days.) MN 166 was very well tolerated in Phase II study: 89% (264 of 297) of subjects completed the first 12 months of the study 82.5% (245 of 297) of subjects completed the full 24 months of the study GI adverse effects as a group and depression were the only adverse events to occur more frequently in MN 166 treated than in placebo treated subjects 16 P Value: 0.044 P Value: 0.030 MN 166 Targets Primarily MN 166 Targets Primarily Chronic Aspects of MS Chronic Aspects of MS P Value: 0.026 P Value: 0.011 MediciNova, Inc. 2008 N=71 1.59 Chronic Efficacy Demonstrated: Chronic Efficacy Demonstrated: Effects on Brain Volume Effects on Brain Volume N=70 1.79 N=34 2.08 N=45 2.12 Percent Brain Volume Reduction Percent Brain Volume Reduction (0 24 months) Brain volume loss was significantly less (p=0.030) in patients receiving 60 mg per day of MN 166 for 24 months compared to the other treatment groups 17 MediciNova, Inc. 2008 Parameter Treatment Groups Placebo 30 mg/day 60 mg/day Number Patients w.

There is no cure for the disease. Multiple Sclerosis Market: Over $8.2 B worldwide sales in 2007* Current Standard of Care: Beta interferons (Rebif, Avonex, Betaserone), Copaxone , Tysabri Administered either by intramuscular or subcutaneous injection or infusion Multiple Sclerosis Multiple Sclerosis *Source: MedAdNews, July 2008 MediciNova, Inc. 2008 14 MN 166: Anti inflammatory and neuroprotective properties in vitro and in vivo Demonstrated effects on brain volume and lesion evolution to axonal damage Targets primarily chronic aspects of multiple sclerosis Oral administration Mechanisms of Action: Stimulates Neurotrophic Growth Factor Release Inhibits nitric oxide and reactive oxygen species production Inhibits Th1 cytokine production (IFN , TNF , IL 1 , IL 6) Pilot studies found reduced relapse rate and Th1 Th2 cytokine shift Phosphodiesterase IV and Leukotriene inhibitor MN 166: A New Approach to MN 166: A New Approach to Treating Multiple Sclerosis Treating Multiple Sclerosis MediciNova, Inc. 2008 Placebo controlled, randomized, double blind Phase II study: Year 1 0, 10 mg tid, 20 mg tid Year 2 10 mg tid, 20 mg tid n ~ 100 MS patients/group 25 sites in Serbia, Ukraine, Belarus, Bulgaria and Romania Key inclusion criteria: Males or females aged 18 to 55 years, with relapsing remitting (RR) and/or secondary progressive (SP) Multiple Sclerosis with continued relapses; A definite diagnosis of relapsing MS using the new International Committee recommendations (MacDonald Criteria); One MRI scan taken two weeks prior to treatment start using a standardized MRI protocol with at least one Gd enhancing lesion; An EDSS score of 5.5 or less at the screening and baseline visits.

Better delivery system (IV) = Better Bioavailability 2. Greater selectivity for 2 receptors in the lungs (better binding) 3. Partial agonist for 1 receptor in the heart MN 221: A New Approach to Treating MN 221: A New Approach to Treating Acute Exacerbations of Asthma Acute Exacerbations of Asthma MediciNova, Inc. 2008 7 Human Human Adrenergic Receptor Adrenergic Receptor Selectivity Selectivity Test Drug 1 IC 50 (M) 2 IC 50 (M) 2 Adrenoceptor Selectivity (IC 50 for 1 / IC 50 for 2 ) Levalbuterol 7.40E 06 1.40E 06 5.3 Albuterol 9.40E 06 1.60E 06 5.9 Terbutaline 6.00E 05 6.50E 06 9.2 MN 221 5.90E 06 1.40E 07 42.4 MediciNova, Inc. 2008 Effect on Heart rate: Effect on Heart rate: Combination of MN 221 Albuterol in Dogs Combination of MN 221 Albuterol in Dogs 8 MediciNova, Inc. 2008 9 MN 221 CL 004 Study Design Randomized, placebo controlled, double blind, dose escalation 23 subjects with mild to moderate stable asthma (FEV 1 60% predicted) Doses tested (all for 15 minutes): 0.35 g /min 1.0 g /min 3.5 g/min 10 g/min MN 221: Positive Phase IIa MN 221: Positive Phase IIa Data Data MN 221 CL 005 Study Design Randomized, single blind, placebo controlled, dose rate escalation 17 subjects with moderate to severe stable asthma (40% FEV 1 75% predicted) Two doses tested: 16 g /min for 15 minutes followed by 8 g /min for 105 minutes (2 hour infusion with toal dose of 1,080 g) or placebo 30 g /min for 15 minutes followed by 15 g/min for 45 minutes (1 hour infusion with a total dose of 1,125 g) or placebo MN 221 CL 004 and MN 221 CL 005 Safety Data: No clinically significant cardiovascular, ECG or vital sign changes, or other safety concerns observed at any dose tested 16 g/min 30 g/min 60 g/min MediciNova, Inc. 2008 Mean Change in FEV Mean Change in FEV 1 1 Study: MN 221 CL 004 Study: MN 221 CL 004 10 Mean Baseline: 77.83% 77.67% 76.78% 81.60% 74.66% 75.78% 78.07% 79.78% At 15 Minutes: 77.54% 79.45% 80.06% 85.74% 82.02% 83.90% 89.65% 88.04% % Predicted: 0.29% 1.78% 3.28% 4.14% 7.36% 8.12% 11.58% 8.26% P = 0.0106 P = 0.0006 P 0.0001 P 0.0001 P 0.0001 P = 0.11 P = 0.07 Placebo 0.35 g/min 1.0 g/min 3.5 g/min 10 g/min 16 g/min 30 g/min 60 g/min MediciNova, Inc. 2008 Mean Change in FEV Mean Change in FEV 1 1 Study: MN 221 CL 005 Study: MN 221 CL 005 11 Mean Baseline: 69.4% Mean Baseline: 64.6% Mean: 81.5% Mean: 82.0% Placebo Mean Baseline: 68.6% MediciNova, Inc. 2008 MN 221 CL 006: Phase IIb study commenced to test efficacy of MN 221 in acute exacerbations of asthma patients (~36 patients in 8 sites) in the emergency department Randomized, modified single blind, placebo controlled, dose escalation study Doses: 16 g/min x 15 min (240 g) 30 g/min x 15 min (450 g) 16 g/min x 15 min; 8 g/min x 105 min (1,080 g) MN 221: Near Term Clinical MN 221: Near Term Clinical Milestone Milestone 12 MediciNova, Inc. 2008 13 Definition: Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system (CNS), affecting approximately 500,000 people in the United States and 2 million people worldwide.

In addition, MediciNova will pursue a variety of initiatives to monetize its remaining product candidates. Business Model: Business Model: Return On Investment Return On Investment MediciNova, Inc. 2008 5 Definition: Long lasting and severe asthma episode that is not responsive to initial bronchodilator or corticosteroid therapy Market Opportunity: Approximately 2 million emergency room visits in the US each year* 500,000 hospitalizations in the US Approximately 4,000 deaths annually in the US* Potential $500 M market opportunity for MediciNova Current Standard of Care (SOC): Beta agonists (all patients) Inhaled or nebulized Corticosteroids (66 77% of patients) IV or oral *Source: National Center for Health Statistics / CDC Acute Exacerbations of Asthma Acute Exacerbations of Asthma MediciNova, Inc. 2008 6 MN 221: A novel, highly selective 2 adrenergic receptor agonist Three Potential Advantages over current therapy 1.

Continue internal development of compound towards commercialization 2. Seek partnership for further development of compound MediciNova has focused its resources on its two prioritized product candidates, MN 221 and MN 166. Following completion of the Phase II trial of MN 166, MediciNova will not pursue further significant clinical development of MN 166 until a partnership is secured.

MediciNova, Inc. *Source: MedAdNews, July 2008 MNOV Headquarters: San Diego, CA Key Financials: Dual listed company on NasdaqGM and Osaka Securities Exchange Hercules ~$27.2M Market Cap as of 9/30/08 ~$55.8M Cash, Cash Equivalents and Marketable Securities as of 6/30/08 MediciNova, Inc. 2008 4 In License: Product candidates with significant clinical or preclinical data Conduct Proof of Concept Clinical Trials: Conduct Phase I and Phase II clinical trials to demonstrate efficacy of compound Two Pathways Towards ROI After Phase II: 1.

Undue reliance should not be placed on these forward looking statements, which speak only as of the date hereof. MediciNova disclaims any intent or obligation to revise or update these forward looking statements. Forward Looking Statements Forward Looking Statements MediciNova, Inc. 2008 3 Development Company Focused on Differentiated Product Candidates Unique access to differentiated, potentially high value assets primarily from Japanese alliances New Approaches to Treat Serious Medical Conditions: MN 221: IV Acute Exacerbations of Asthma candidate Potential $500 M US opportunity for MediciNova MN 166: Oral Multiple Sclerosis candidate In 2007, over $8.2B in worldwide MS therapeutic sales* Corporate Overview: Corporate Overview: MediciNova, Inc.

These forward looking statements may be preceded by, followed by or otherwise include the words believes, expects, anticipates, intends, estimates, projects, can, could, may, would, or similar expressions. Actual results or events may differ materially from those expressed or implied in any forward looking statements due to various factors, including, without limitation, the risks and uncertainties inherent in clinical trials and product development and commercialization, such as the uncertainty in results of clinical trials for product candidates, the uncertainty of whether the results of clinical trials will be predictive of results in later stages of product development, the risk of delays or failure to obtain or maintain regulatory approval, the risk of failure of the third parties upon whom MediciNova relies to conduct its clinical trials and manufacture its product candidates to perform as expected, the risk of increased cost and delays due to delays in the commencement, enrollment, completion or analysis of clinical trials or significant issues regarding the adequacy of clinical trial designs or the execution of clinical trials and the timing, cost and design of future clinical trials and research activities; the timing of expected filings with the FDA; MediciNova s failure to execute strategic plans or strategies successfully; MediciNova s collaborations with third parties; the availability of funds to complete product development plans and MediciNova s ability to raise sufficient capital when needed; intellectual property or contract rights; and the other risks and uncertainties described in MediciNova s filings with the Securities and Exchange Commission, including MediciNova s annual report on Form 10 K for the year ended December 31, 2007 and its subsequent periodic reports on Forms 10 Q and 8 K.

These forward looking statements include, without limitation, statements regarding MediciNova s clinical trials supporting safety and efficacy of product candidates and the potential novelty of such product candidates as treatments for disease, plans and objectives for clinical trials and product development, strategies, future performance, financial condition, liquidity and capital resources.

MediciNova, Inc. 2008 Accelerating the global development and commercialization of innovative pharmaceuticals Exhibit 99.1 MediciNova, Inc. 2008 Statements in this presentation that are not historical in nature constitute forward looking statements within the meaning of the safe harbor provisions of the Private Securities Litigation Reform Act of 1995.