MediciNova, Inc. 2009 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 pr

Secure a global partnership for MN 166/AV 411 combined package* 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** Investment Highlights Investment Highlights Note: Development plans / timelines for MN 221 clinical trials are subject to change *Assumes completion of acquisition of Avigen **Anticipated completion dates based on current projections

Anticipated completion in 2H, 2010* MN 221 CL 007 MN 221 CL 007 23 Note: Development plans / timelines for MN 221 clinical trials are subject to change *Anticipated completion dates based on current projections MediciNova, Inc. 2009 MN 221 CL 010 (COPD) MN 221 CL 010 (COPD) 24 Note: Development plans / timelines for MN 221 clinical trials are subject to change *Anticipated completion dates based on current projections Doses: 150 g in 15 minutes followed by 150 g in 45 minutes (1 hour infusion with a total dose of 300 g) or placebo 300 g in 15 minutes followed by 300 g in 45 minutes (1 hour infusion with a total dose of 600 g) or placebo 600 g in 15 minutes followed by 600 g/min in 45 minutes (1 hour infusion with a total dose of 1,200 g) or placebo Study Design Randomized, double blind, placebo controlled Phase Ib dose escalation study 48 subjects with stable moderate to severe Chronic Obstructive Pulmonary Disease (FEV 1 30% 80% and FEV 1 /FVC ratio 0.7) at 6 sites in the US Outcome measures descriptive statistics only FEV 1 , PK, safety Anticipated completion in 1H, 2010 MediciNova, Inc. 2009 25 Commercially Attractive Commercially Attractive Diversified Portfolio Diversified Portfolio COPD COPD Asthma Asthma Seeking Global Partner Seeking Global Partner MediciNova, Inc. 2009 26 Leadership Years Experience Background Yuichi Iwaki, MD, PhD Yuichi Iwaki, MD, PhD CEO President 33 Professor at USC, formerly Professor at University of Pittsburgh; Advisor to JAFCO, Tanabe Shintaro Shintaro Asako, Asako , , Chief Financial Officer 11 KPMG USA (Audit), Arthur Andersen USA Masatsune Masatsune Okajima, Okajima , , VP, Head of Japanese Office 17 Daiwa Securities SMBC, Sumitomo Capital Securities, Sumitomo Bank Management Team with Management Team with Global Experience Global Experience Clinical Development Consultant Board Member 26 CEO of Panacos Metaphore; President of the Janssen Research Foundation, a J J company CPA CMA Alan Dunton, MD, PhD MediciNova, Inc. 2009 27 Near Term Business Plan: 1.

What have we learned? MediciNova, Inc. 2009 MN 221 CL 006 MN 221 CL 006 Hospitalization Rate by Treatment Group Hospitalization Rate by Treatment Group 22 MN 221 reduced the hospitalization rate by 45% MediciNova, Inc. 2009 Study Design Randomized, placebo controlled, double blind, multi center Phase II clinical trial 200 patients with severe, acute exacerbations of asthma (FEV 1 50% predicted) at ~45 Emergency Department sites in US, Canada, Australia, and New Zealand Dose Groups (~100 patients/group): 600 g in 15 minutes; 600 g for in minutes (1,200 g ) MN 221 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 MN 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 trial. MN 221 CL 006: MN 221 CL 006: What have we learned?

CL 006, CL 007 located in the Emergency Department MediciNova, Inc. 2009 MN 221 CL 004: MN 221 CL 004: Mean Change in FEV Mean Change in FEV 1 1 19 p 0.05 p 0.0001 p 0.0001 p 0.0001 p 0.001 Baseline: 77.83% 77.67% 76.78% 81.60% 74.78% 75.78% 78.07% 79.78% MediciNova, Inc. 2009 MediciNova, Inc. 2009 MN 221 CL 005: MN 221 CL 005: Mean Change in FEV Mean Change in FEV 1 1 20 Baseline: 64.57% Baseline: 69.35% Mean: Mean: 82.04% 82.04% Mean: Mean: 81.47% 81.47% Baseline: 68.64% Baseline: 68.64% MediciNova, Inc. 2009 21 What did we learn from MN 221 CL 006?

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. 2009 16 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. 2009 Effect on Heart rate: Effect on Heart rate: Combination of MN 221 Albuterol Combination of MN 221 Albuterol in Dogs in Dogs 17 MediciNova, Inc. 2009 MN 221 Clinical Trials MN 221 Clinical Trials 18 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 Number Patients Patients 23 17 29 200 48 Number Sites Number 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 the clinic.

Open IND for ibudilast AV 411 trial supports MN 166 dosing up to 100 milligrams (mg) versus the maximum dosing of 60 mg in the Phase 2 trial for MN 166 Expected time savings of six to twelve months. Analog compounds behind ibudilast First generation development candidate: AV1013 Second generation dual target leads AV 411 Package: New Indication AV 411 is currently being studied for Opioid Withdrawal Ongoing clinical study run jointly by the New York State Psychiatric Institute and Columbia University in NYC Additional Additional Value Value from from Avigen Avigen Deal Deal MediciNova, Inc. 2009 14 Definition: Asthma Exacerbations: Long lasting and severe asthma episode that is not responsive to initial bronchodilator or corticosteroid therapy 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 Thousands MediciNova, Inc. 2009 15 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.

New Lesions at Month 2 72 64 56 Total Number New Lesions in all Patients at Month 2 426 338 315 Total Number of Persistent Black Holes at Month 10 98 58 47 Percentage of Lesions Evolving to PBH at Month 10 23% 17% 14% P Value 0.036 0.004 Reduction of Persistent Black Hole Reduction of Persistent Black Hole (PBH) Formation (PBH) Formation 10 MediciNova, Inc. 2009 New T1 gadolinium enhancing or new T2 lesions were defined as new lesion in the first on study MRI at month 2 Lesions that were hypointense and inactive at month 10 were PBH Relative Risk (RR) of new lesion evolution to PBH was analyzed using a general linear model with the error term from the Poisson distribution MediciNova, Inc. 2009 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 11 4.1% 5.3% 8.0% MediciNova, Inc. 2009 12 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. 2009 13 AV 411 Package: Value to Potential MN 166 Partnership Both AV 411 and MN 166 are ibudilast AV 411 preclinical data expected to support clinical package for MN 166.

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 7 MediciNova, Inc. 2009 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: 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 8 MN 166 Targets Primarily MN 166 Targets Primarily Chronic Aspects of MS Chronic Aspects of MS Note: In general, P Values listed on this slide compare Placebo group to 60mg/day group of MN 166 P Value: 0.04 P Value: 0.035 ~50% reduction P Value: 0.004 P Value: 0.09 P Value: 0.08 MediciNova, Inc. 2009 Brain volume changes are linked to axonal loss 9 MN 166 MN 166 Chronic Efficacy Chronic Efficacy Demonstrated: Effects on Brain Volume Demonstrated: Effects on Brain Volume Parameter Treatment Groups Placebo 30 mg/day 60 mg/day Number Patients w.

(2) Assumes the convertible notes convert to MediciNova shares at $6.80. (3) Assumes all convertible notes are converted into MediciNova shares on the first monthly conversion date. Sources of information: SEC Edgar Filings MediciNova, Inc. 2009 6 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 Anti inflammatory Inhibits PDE4, Leukotriene, and Th1 cytokine production (TNF alpha, IL 1beta, IL 6) Stimulates Th2 cytokine production (IL 4, IL 10) 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. 2009 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.

Notes (2) (3) 100% Conv. Notes (2) (3) Common Stock Equivalents MediciNova Stockholders 12,048,003 12,048,003 12,048,003 12,048,003 Avigen Stockholders 2,717,712 5,435,424 MediciNova Exercisable Options 1,711,350 1,711,350 1,711,350 1,711,350 13,759,353 13,759,353 16,477,065 19,194,777 Ownership % MediciNova Stockholders 87.6% 87.6% 73.1% 62.8% Avigen Stockholders 0.0% 0.0% 16.5% 28.3% MediciNova Exercisable Options 12.4% 12.4% 10.4% 8.9% 100.0% 100.0% 100.0% 100.0% (1) Assumes first payment consideration and second payment consideration aggregate $37.0 million and are both paid at closing and that MediciNova issues no shares or options from August 20, 2009 through the first conversion date of the convertible notes.

Actual ownership of MediciNova shares will depend on a variety of factors, including the actual amounts of the First Payment Consideration and Second Payment Consideration and the rounding of fractional shares set forth in the indenture governing the convertible notes. Summary Securities Ownership Review (Fully Diluted Basis) Pre Transaction Pro Forma Shares Outstanding Post Transaction (1) Consideration Shares All Cash 50% Cash 50% Conv.

The notes can be converted on a monthly basis into common shares of MediciNova at an initial conversion price equal to $6.80. Avigen Avigen Transaction Overview Transaction Overview Pro Forma Stockholder Review Pro Forma Stockholder Review 5 This pro forma ownership review is presented for illustrative purposes only and does not indicate actual ownership of MediciNova shares at any past, present, of future date.

This holdback amount is being held for any adjustments to certain Avigen defined expenses, marketable security risk, sub tenant risk, and other liabilities in excess of amounts agreed by the parties. Convertible Notes Consideration 18 month maturity from the date of closing of merger (no early cash redemption). Principal from the notes will be held in a trust account with principal invested in certain approved investment options.

MediciNova, Inc. *Source: Individual annual reports of leading MS companies, 2008 MNOV Headquarters: San Diego, CA 4 Merger Consideration Each Avigen stockholder will have the option of receiving their pro rata allocation of cash or convertible notes aggregating approximately $37.0 million ($1.24/share) , subject to potential upward and downward adjustments as set forth in the merger agreement: First payment consideration of approximately $35.5 million ($1.19/share) ; and Second payment consideration of approximately $1.5 million (~$0.05/share) payable on June 30, 2010.

Investors and security holders will be able to obtain free copies of any documents filed with the SEC by MediciNova, Inc. and Avigen, Inc. through the website maintained by the SEC at http://www.sec.gov. MediciNova, Inc. 2009 3 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: oral multiple sclerosis candidate In 2008, over $8B in worldwide MS therapeutic sales* Key Financials: Dual listed company on NasdaqGM and Osaka Securities Exchange Hercules ~$37.2 million net Cash, Cash Equivalents and Marketable Securities as of 9/30/2009 ~$75.2 million Market Cap (NasdaqGM) as of 11/09/2009 ~12 million shares outstanding Corporate Overview: Corporate Overview: MediciNova, Inc.

This material is not a substitute for the registration statement/prospectus/proxy statement MediciNova, Inc. and Avigen, Inc. will file with the SEC or any other documents that the parties may file with the SEC and send to their respective shareholders in connection with the transaction. INVESTORS AND SECURITY HOLDERS OF AVIGEN, INC. ARE URGED TO READ ANY SUCH DOCUMENTS FILED WITH THE SEC CAREFULLY IN THEIR ENTIRETY WHEN THEY BECOME AVAILABLE BECAUSE THEY WILL CONTAIN IMPORTANT INFORMATION ABOUT THE TRANSACTION.

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. This communication does not constitute an offer to sell or the solicitation of an offer to buy any securities or a solicitation of any vote or approval.

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 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; failure to complete the merger with Avigen, Inc. on a timely basis or at all; 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, 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 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, anticipated benefits of the merger with Avigen, Inc., value and benefits to stockholders from such transaction, strategies, future performance, financial condition, liquidity and capital resources.

MediciNova, Inc. 2009 Accelerating the global development and commercialization of innovative pharmaceuticals Exhibit 99.1 MediciNova, Inc. 2009 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.