Accelerating the global development and commercialization of innovative pharmaceuticals MediciNova, Inc. 2010 Forward Looking Statements Forward Looking Statements Statements in this presentation that are not historical

Secure a global partnership for MN 166 (AV411) 2. Secure a regional partnership (ex US/Japan rights) for MN 221 Clinical Milestones: 1. MN 221 CL 007 Phase II Study for Acute Exacerbations of Asthma Anticipated completion 2H, 2010* 2. MN 221 CL 010 Phase Ib Study in Moderate to Severe COPD Patients Anticipated completion in 1H, 2010* 3. Ongoing AV411 Study for Opioid Withdrawal Anticipated completion in 1H, 2010* Investment Highlights Investment Highlights *Anticipated completion dates based on current projections Note: Development plans / timelines for MN 221 clinical trials are subject to change

Glial cell activation contributes to reward and withdrawal aspects of opioids and the development and maintenance of neuropathic pain. AV411 represents a new pharmocotherapy approach for drug addiction and neuropathic pain. Additional Value from Avigen Additional Value from Avigen Deal Deal MediciNova, Inc. 2010 24 AV411: Ongoing clinical trial Study Objective: Assess AV411 safety/tolerability/PK and preliminary efficacy for opiate withdrawal in heroin dependent subjects Ongoing clinical trial run jointly by the New York State Psychiatric Institute and Columbia University in NYC (Investigator IND study; MediciNova is not the sponsor) Trial to enroll ~30 patients (10 completers/cohort) Anticipated completion in 1H, 2010* AV411: Opioid AV411: Opioid Withdrawal Withdrawal Trial Design/Endpoints Week 1 2 3 Treatment Morphine (30 mg QID) and Placebo BID Morphine (30 mg QID) and Placebo BID or 20 mg BID of Ibudilast or 40 mg BID of Ibudilast Placebo BID or 20 mg BID of Ibudilast or 40 mg BID of Ibudilast Endpoints Safety, Tolerability, PK Safety, Tolerability, PK Withdrawal scores, Safety, Tolerability, PK Note: QID refers to taking the medication four times per day; BID refers to taking the medication twice a day *Anticipated completion date based on current projections MediciNova, Inc. 2010 25 Commercially Attractive Commercially Attractive Diversified Portfolio Diversified Portfolio MediciNova, Inc. 2010 26 Leadership Years Experience Background Yuichi Iwaki, MD, PhD Yuichi Iwaki, MD, PhD CEO President 34 Professor at USC, formerly Professor at University of Pittsburgh; Advisor to JAFCO, Tanabe Shintaro Shintaro Asako, Asako , , CPA Chief Financial Officer 12 KPMG USA (Audit), Arthur Andersen USA Masatsune Masatsune Okajima, Okajima , , CMA VP, Head of Japanese Office 18 Daiwa Securities SMBC, Sumitomo Capital Securities, Sumitomo Bank Management Team with Management Team with Global Experience Global Experience Alan Dunton, MD, PhD Clinical Development Consultant Board Member 27 CEO of Panacos Metaphore; President of the Janssen Research Foundation, a J J company MediciNova, Inc. 2010 27 Near Term Business Plan: 1.

MediciNova, Inc. 2010 22 Acute Efficacy Demonstrated: Acute Efficacy Demonstrated: Time to First Relapse Time to First Relapse Median 401 days Median 244 days P Value: 0.044 Plot of Time to First Relapse by Treatment (ITT) Core (Year 1) MediciNova, Inc. 2010 23 AV411: Value to MediciNova Both AV411 and MN 166 are ibudilast API and drug product supply 4 completed Phase I and Ib/IIa clinical trials Open IND for ibudilast (Analgesia, Addiction) Clinical preclinical support for MN 166 dosing up to 100 mg/day 2 method of use patents issued in 2009; multiple filings in progress Analog compounds behind ibudilast First generation development candidate: AV1013 composition of matter patent issued Second generation dual target leads Opioid Withdrawal Neuropathic Pain Indications Ibudilast is a good glial cell attenuator in vitro and in the central nervous system (CNS) in vivo.

New Lesions (NL) at Month 2 72 64 56 Total Number of NLs in all Patients at Month 2 426 338 315 Total Number of Persistent Black Holes (PBH) at Month 10 98 58 47 Percentage of Lesions Evolving to PBHs at Month 10 23% 17% 14% Percent Reduction from Placebo Group 26% 39% 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 Formation Formation 20 MediciNova, Inc. 2010 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 21 4.1% (49% Reduction) 5.3% (34% Reduction) 8.0% Sustained disability progression was significantly less likely (~50%) in those patients receiving MN 166 at 30 or 60 mg per day for 24 months than in those patients receiving the drug for 12 months (p=0.026).

Safety Profile: 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 Adverse effects reported more frequently in MN 166 treated than placebo treated subjects: GI effects depression Completed Clinical Study: Completed Clinical Study: MN 166 CL 001 MN 166 CL 001 17 MediciNova, Inc. 2010 18 P Value: 0.04 P Value: 0.035 MN 166 Targets Primarily MN 166 Targets Primarily Chronic Aspects of MS Chronic Aspects of MS P Value: 0.026 P Value: 0.004 P Value: 0.09 P Value: 0.08 Note: P values listed on this slide compare placebo group to 60mg/day group of M N 166 Indicative of Potential Neuroprotective Effect: Reduced brain volume loss Reduced conversion of acute lesions to persistent black holes Sustained disability progression was significantly less likely Acute Clinical Benefit: Prolong time to relapse (by 127 days.) Annualized relapse rate Protocol Defined Primary Endpoint (Surrogate Endpoint): No significant reduction in the cumulative number of active (gadolinium enhancing (T1) and non enhancing new/enlarging (T2)) lesions on cranial MRI scans over 12 months of treatment was observed Positive trends were observed in volume of gadolinium enhancing (T1) lesions MediciNova, Inc. 2010 Brain volume changes are linked to axonal loss 19 MN 166 MN 166 Chronic Efficacy Chronic Efficacy Demonstrated: Effects on Brain Volume Demonstrated: Effects on Brain Volume 1.20% MediciNova, Inc. 2010 Parameter Treatment Groups Placebo 30 mg/day 60 mg/day Number Patients w.

Anticipated completion in 2H, 2010* MN 221 CL 007: MN 221 CL 007: Study Design Study Design 14 Note: Development plans / timelines for MN 221 clinical trials are subject to change Anticipated completion date based on current projections MediciNova, Inc. 2010 Randomized, double blind, placebo controlled Phase Ib dose escalation study 48 subjects with stable moderate to severe COPD (FEV 1 30% 80% and FEV 1 /FVC ratio 0.7) at 6 sites in the US Doses: 300 g MN 221 over 1 hour (150 g in 15 minutes; 150 g in 45 minutes) or placebo 600 g MN 221 over 1 hour (300 g in 15 minutes; 300 g in 45 minutes) or placebo 1,200 g MN 221 over 1 hour (600 g in 15 minutes; 600 g in 45 minutes) or placebo Outcome measures descriptive statistics only FEV 1 , PK, safety Anticipated completion in 1H, 2010 MN 221 CL 010 (COPD): MN 221 CL 010 (COPD): Study Design Study Design 15 Note: Development plans / timelines for MN 221 clinical trials are subject to change *Anticipated completion date based on current projections MediciNova, Inc. 2010 16 MN 166 for Multiple Sclerosis (MS): Oral administration Multiple mechanisms of action, both neuroprotective and anti inflammatory MN 166 targets primarily chronic aspects of MS Benign safety profile Mechanisms of Action: Potentially Neuroprotective Inhibits nitric oxide and reactive oxygen species production Stimulates release of neuronal growth factors Reduces demyelination Anti inflammatory Inhibits PDE s and MIF, leukotriene release, proinflammatory cytokines (TNFa, IL 1b, MCP, IL 6) Can increase IL 10 release Current Standard of Care: Beta interferons (Rebif , Avonex , Betaseron/Betaferon ), Copaxone , Tysabri Primary focus is on acute treatment of MS symptoms (i.e., relapse rate) MN 166 for the Treatment of MN 166 for the Treatment of Multiple Sclerosis Multiple Sclerosis MediciNova, Inc. 2010 Placebo controlled, Randomized, Double blind Phase II Study: Year 1 Placebo, 30 mg/day, 60mg/day Year 2 30 mg/day, 60mg/day 297 patients (~100 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; One MRI scan taken two weeks prior to treatment start using a standardized MRI protocol with at least one Gd enhancing lesion; An Expanded Disability Status Scale (EDSS) score of 5.5 or less at the screening and baseline visits.

MN 221 CL 006: MN 221 CL 006: What have we learned? What have we learned? MediciNova, Inc. 2010 MN 221 CL 006: MN 221 CL 006: Hospitalization Rate by Treatment Group Hospitalization Rate by Treatment Group 13 MN 221 reduced the hospitalization rate by 45% Note: SOC means standard of care. MediciNova, Inc. 2010 Randomized, placebo controlled, double blind, multi center Phase II clinical trial 200 patients with severe, acute exacerbations of asthma (FEV 1 50% predicted) at ~35 Emergency Department sites in US, Canada, Australia, and New Zealand Dose Groups (~100 patients/group): 1,200 g MN 221 over 1 hour (600 g in 15 minutes; 600 g in 45 minutes) Placebo Patients will receive Standard of Care (SOC) treatment in addition to adjunctive treatment with MN 221 or placebo Primary efficacy endpoint will be improvement in FEV 1 (% predicted) at 5 hours The study is designed to have 80% power to detect a treatment difference of 5 percentage points in FEV 1 (% predicted) when comparing M N 221 + SOC to Placebo + SOC at a two sided level of 0.05.

There were no safety concerns with adding MN 221 to the standard of care. There was a reduction in the hospitalization rate among patients treated with MN 221. Overall, improvement in FEV 1 was greater for patients receiving MN 221 than placebo. A dose of 1,200 g of MN 221 administered over one hour was selected for the MN 221 CL 007 clinical trial.

CL 006, CL 007 located in emergency departments. MediciNova, Inc. 2010 MN 221 CL 004: MN 221 CL 004: Mean Change in FEV Mean Change in FEV 1 1 10 p 0.05 p 0.001 p 0.05 p 0.001 MediciNova, Inc. 2010 MN 221 CL 005: MN 221 CL 005: Mean Change in FEV Mean Change in FEV 1 1 11 Baseline: 64.6% Baseline: 69.4% 1 Hour: 82.0% 2 Hours: 81.5% Baseline: 68.6% Baseline: 68.6% 1 Hour: 70.5% 2 Hours: 71.2% MediciNova, Inc. 2010 12 What did we learn from the MN 221 CL 006 clinical trial?

Improved Efficacy Route of Administration (IV v. Inhalation) 2. Improved Safety Higher selectivity for 2 receptor than 1 Partial agonist for 1 receptor 3. Reduced Health Care Expenses MediciNova, Inc. 2010 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. 2010 Effect on Heart rate: Effect on Heart rate: Combination of MN 221 Albuterol Combination of MN 221 Albuterol in Dogs in Dogs 8 MediciNova, Inc. 2010 MN 221 Clinical Trials MN 221 Clinical Trials 9 Completed Studies Completed Studies Ongoing Studies Ongoing Studies CL 004 CL 005 CL 006 CL 007 CL 010 Indication Indication Mild to moderate Asthmatics Moderate to Severe Asthmatics Acute Exacerbations of Asthma Acute Exacerbations of Asthma Moderate to Severe COPD patients FEV FEV 1 1 (Entry Criteria) (Entry Criteria) FEV 1 60% 75% FEV 1 40% FEV 1 55% FEV 1 50% 80% FEV 1 30% Number of Number of Patients Patients 23 17 29 200 48 Number of Number of Sites Sites 4 4 8 ~45 6 Doses Tested Doses Tested Compared to Compared to Placebo Placebo 5.25, 15, 52.5, 150, 240, 450, 900 g over 15 min 1080 g over 2 hr; 1,125 g over 1 hr 240, 450 g over 15 min; 1080 g over 2 hr 1200 g over 1 hr 300, 600, 1200 g over 1 hr Note: CL 004, CL 005, CL 010 located in clinical sites.

Actual ownership of MediciNova shares will depend on a variety of factors, including the actual amount of the Second Payment Consideration, the rounding of fractional shares set forth in the governing the convertible notes and the number of holders electing to convert their convertible notes into MediciNova shares. MediciNova, Inc. 2010 5 Definition: Acute Asthma Exacerbations: Long lasting and severe asthma episodes that are not responsive to initial bronchodilator or corticosteroid therapies COPD Exacerbations: Sustained worsening of the patient's condition, from the stable state and beyond normal day to day variations, that is acute in onset Market Opportunity: Potential $1 billion+ combined market opportunity worldwide* (acute asthma COPD exacerbations) Current Standard of Care (SOC): Beta agonists Inhaled Anticholinergics Inhaled Corticosteroids IV or oral Source: National Center for Health Statistics / CDC, WHO website, Core Health indicators MN 221 for Exacerbations of MN 221 for Exacerbations of Acute Asthma and COPD Acute Asthma and COPD COPD Discharged Hospitalized 72% 28% ~1.9 million Asthma 52% 48% ~1.5 million Hospitalization Rates Amongst Asthma and COPD Patients *Source: Internal MediciNova projections MediciNova, Inc. 2010 6 MN 221: A New Approach to Treating MN 221: A New Approach to Treating Exacerbations of Acute Asthma COPD Exacerbations of Acute Asthma COPD MN 221: A novel, highly selective 2 adrenergic receptor agonist Three potential advantages over current therapy: 1.

Common Stock Equivalents # Shares MediciNova Stockholders 12,172,510 Avigen Stockholders (1st payment consideration) 4,330,268 Avigen Stockholders (2nd payment consideration) 134,325 MediciNova Exercisable Options 1,319,391 Total 17,956,494 Ownership % MediciNova Stockholders 67.8% Avigen Stockholders (both pmt. considerations) 24.9% MediciNova Exercisable Options 7.3% Total 100.0% Potential Cash Available to MediciNova (Conversion price of $6.80 per MNOV share) First Payment Consideration ( ~$1.19/share) $29,445,824.82 Second Payment Consideration ( ~$0.04/share) $913,408.56 Total Cash Potentially Available to MediciNova $30,359,233.38 This pro forma ownership table is presented for illustrative purposes only and does not indicate actual ownership of MediciNova shares at any past, present, of future date.

MediciNova, Inc. **Source: Individual annual reports of leading MS companies, 2008 *Source: Internal MediciNova projections Pro Forma Summary of Securities Ownership Potential Financing from Avigen as of 12/31/2009 Acquisition 4 Pro Forma Stockholder Review Pro Forma Stockholder Review Note: Assumes Second Payment Consideration in the amount of $1.1 million was paid at closing, that all convertible notes, including those issued as part of the Second Payment Consideration, were converted on December 31, 2009 and that no rounding of fractional shares occurred as part of the conversion calculations.

You are cautioned not to place undue reliance on these forward looking statements, which speak only as of the date January 11, 2010. MediciNova disclaims any intent or obligation to revise or update these forward looking statements. MediciNova, Inc. 2010 3 MediciNova Overview: Founded in September 2000 Headquartered in San Diego, CA Additional office in Tokyo, Japan Dual listing on NasdaqGM as MNOV and Osaka Securities Exchange as 4875 $85.7 million Market Cap (NasdaqGM) as of 12/31/2009 Development Company Focused on Differentiated Product Candidates Unique access to differentiated, potentially high value assets primarily from Japanese alliances (Kyorin, Kissei, Mitsubishi Tanabe Pharma, Meiji) New Approaches to Treat Serious Medical Conditions: MN 221: Intravenous (IV) acute asthma and COPD candidate Potential $1 billion+ combined market opportunity worldwide* MN 166 (AV411): oral multiple sclerosis candidate; additional enabled neurological conditions In 2008, over $8 billion 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, will, 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 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; MediciNova s ability to realize the anticipated strategic and financial benefits from its acquisition of Avigen, Inc., to integrate the two ibudilast development programs and to pursue discussions with potential partners to secure a strategic collaboration to advance the clinical development of the combined development program; the availability of funds to complete product development plans and MediciNova s ability to raise sufficient capital when needed, or at all; 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, 2008 and its subsequent periodic reports on Forms 10 Q and 8 K.

These forward looking statements include statements regarding MediciNova s clinical trials supporting the safety and efficacy of its 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, expectations, assumptions, financial condition, liquidity and capital resources.

MediciNova, Inc. 2010 Exhibit 99.1 Accelerating the global development and commercialization of innovative pharmaceuticals MediciNova, Inc. 2010 Forward Looking Statements Forward Looking Statements 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.