Non Confidential Presentation July 2007 2 This presentation contains forward looking statements that involve risks and uncertainties. These forward looking statements include, but are not limited to, statements regarding

USC, Pitt; Advisor to JAFCO, Tanabe; Director, Avigen, Inc. Richard Gammans, PhD, MBA Chief Development Officer 30 Incara, Indevus, BMS Kenneth W. Locke, PhD Chief Scientific Officer 23 Tanabe Research Laboratories USA, Indevus, Hoechst Shintaro Asako, CPA Chief Financial Officer 8 KPMG USA (Audit), Arthur Andersen USA Masatsune Okajima, CMA VP, Head of Japanese Office 15 Daiwa Securities SMBC, Sumitomo Capital Securities, Sumitomo Bank Lynn Terhorst, MBA VP, Business Planning Analysis 24 Ligand, General Electric Medical Systems, Hybritech, Molecular Biosystems Non Confidential Presentation July 2007 33 Investment Highlights IN LICENSE: Innovative business model ADVANCE: Rich mid to late stage clinical development pipeline with clear market advantages MONETIZE: Near , mid and longer term realization of asset potential COMMERCIALIZE: MN 221 and MN 166 targeted for commercialization* by MediciNova Near term milestones as key value drivers *pending FDA approval

Yes No Zyflo IV (Ph I) No ? Yes Liver Toxicity MN 221 IV (Ph II) Yes Yes Yes No Non Confidential Presentation July 2007 29 Targeted Path to Commercialization* MN 221 MN 166 *pending FDA approval **completed as early as filing as early as Non Confidential Presentation July 2007 30 2007 Milestones Clinical MN 166 Positive Phase II (yr 1) results announced 3/07 MN 305 Proof of concept Phase II results anticipated 07Q3 MN 221 Proof of concept Phase II results anticipated 07Q4 Scientific MN 029 Positive Phase I DCE MRI results to be presented at ECCO (Barcelona, September 23 27) MN 166 Positive Phase II results to be presented at ECTRIMS (Prague, October 11 14) Corporate Prioritization of development pipeline Monetization efforts ongoing (out licensing, etc.) Non Confidential Presentation July 2007 31 Financials Dual Listing: MNOV (Nasdaq) 4875 (Osaka (Hercules)) Cash: $98.1M as of 3/31/07 Sufficient cash through at least 12/31/08 Shares outstanding: 11.6M Market cap as of 7/20/07: ~$100M Non Confidential Presentation July 2007 32 Management Team with Global Experience LEADERSHIP Years Experience Life Sciences Background Yuichi Iwaki, MD, PhD CEO President 31 Prof.

Primary endpoint: change from baseline in mean FEV1 after a 15 minute infusion of MN 221 Initiated December 2006; data anticipated 07Q4 Non Confidential Presentation July 2007 26 Clear Development Path Clinical Plan: Phase IIa results anticipated 07Q4 Phase IIb results as early as 09Q1 Phase III (2 trials) results as early as 10Q2 Modest development costs ($45M to NDA) Well defined regulatory path Acute dosing = short trials Modest number of patients required for NDA (potentially life threatening condition) Possible fast track review NDA filing targeted for as early as 10Q4 Non Confidential Presentation July 2007 27 Favorable Commercial Metrics Market addressable through focused sales force (50 100 reps) Significant market opportunity ($500M) Rapid market penetration (could become new standard of care) High payer acceptance (due to potential reduction in hospitalizations) Non Confidential Presentation July 2007 28 MN 221 Competitive Advantages Compound Dosing Proven Mechanism Rapid Action Reliable Delivery Safety Issues Agonists Inhaled; Nebulized Yes Yes No Cardiovascular (palpitations) Singulair IV (Ph III) No ?

Efficacy Decrease MR lesions, no change in brain volume Reduced relapse rate, fewer MR lesions Decreased Gd enhancing lesions at 720 mg Fewer MR lesions, reduced relapse rate Less brain volume loss, increase time to relapse Side effects heart rate, blood pressure, dyspnea Fever, nausea, vomiting GI disorder, H/A, nasopharyngitis liver enzymes, arthralgia Mild GI disorder Non Confidential Presentation July 2007 21 MN 221 (Status Asthmaticus) Source Kissei Pharmaceutical (2004) Mechanism Highly selective 2 adrenergic receptor agonist Advantages Clinically proven MOA Greater cardiovascular safety Reliable, rapid route of administration (i.v.) Clinical Status Well tolerated in Phase I Phase II started 10/06 Milestones Phase IIa Results anticipated 07Q4 Commercial Strategy MNOV to commercialize in U.S.* pending FDA approval Non Confidential Presentation July 2007 22 MN 221: Status Asthmaticus Definition: Long lasting and severe asthma episode that is not responsive to initial bronchodilator or corticosteroid therapy Market Opportunity: ~1.9 million emergency room visits in the U.S. each year ~500,000 hospitalizations* ~4,000 deaths annually in the U.S.* Current Standard of Care: Beta agonists, inhaled or nebulized (all patients) Corticosteroids, IV or oral (66 77% of pts) *source: National Center for Health Statistics/CDC Non Confidential Presentation July 2007 23 MN 221: New Treatment Paradigm Proven mechanism of action ( 2 adrenergic receptor agonist) Rapid, reliable IV delivery (vs. inhaled/nebulized) Safer (greater selectivity = fewer cardiovascular side effects) Non Confidential Presentation July 2007 24 Human Adrenergic Receptor Selectivity Drug Adrenoceptor (IC 50 , M) 2 Adrenoceptor Selectivity 1 2 (IC 50 for 1 /IC 50 for 2 ) MN 221 1.39 0.0224 62.1 Albuterol (Salbutamol) 5.63 1.56 3.61 S( ) Propranolol 0.00127 0.00094 1.35 Displacement of [ 3 H] cyanopindolol or [ 3 H] CGP12177 binding in membrane preparations expressing human cloned 1 and 2 adrenoceptors, respectively MN 221 selectively binds to human 2 adrenergic receptors Non Confidential Presentation July 2007 25 MN 221 Phase IIa Phase IIa Proof of Concept Randomized, double blind, placebo controlled, sequential dose escalation study Objectives: Determine the efficacy of a single 15 minute treatment Determine the efficacy of two sequential 15 minute treatments 22 mild to moderate asthmatics at 4 centers in the U.S.

Douglas L. Arnold, MD Non Confidential Presentation July 2007 14 MN 166 Orally administered with new controlled release dosage form in development Neuroprotective and Anti inflammatory in replicated pre clinical studies Safe 17 years of clinical use with over 3 million exposures has not revealed rare, concerning safety issues Toxicology package supporting Japanese registration No safety concerns identified in PhII study Non Confidential Presentation July 2007 15 Neuroprotection + Anti inflammatory MN 166 may reduce both relapses (via anti inflammatory effects) and disease progression (via neuroprotection) Non Confidential Presentation July 2007 16 MN 166: Clinical Efficacy Demonstrated neuroprotective and anti inflammatory effects in patients with relapsing MS Neuroprotective outcome: Attenuated % brain volume loss ( .8% vs. 1.2%) Anti inflammatory outcomes: Pilot studies found reduced relapse rate and Th1 Th2 cytokine shift Prolonged time to relapse ( 1 yr) Increased % relapse free (56%) Decreased T1 Gd lesion volume Non Confidential Presentation July 2007 17 Effects on Time to First Relapse Phase III endpoint for certain FDA approved MS products Non Confidential Presentation July 2007 18 Brain volume changes are linked to axonal loss Effects on Brain Volume 1.2 0.79 0 0.2 0.4 0.6 0.8 1 1.2 1.4 Placebo 20mg, TID % Decrease in Brain Volume Non Confidential Presentation July 2007 19 Unmet Need MN 166 Interferon Products More convenient dosing Oral Intravenous or subcutaneous injection (Injection site pain, swelling and itching) Greater efficacy At least comparable efficacy observed in early trials Current relapse reduction rate is ~33% Longer duration of effect No neutralizing antibodies formed; no loss of effect Relative benefit gained from existing drugs may decline over time possibly due to presence of neutralizing antibodies Halt disease progression At least comparable early trends in Phase II Avonex reduced the risk of disease progression by ~37% in patients treated for 2 years compared to placebo Better safety profile Only mild, transient GI side effects noted in Phase II Common side effects include injection site reactions, flu like symptoms, depression, liver problems and blood abnormalities Benefits VS Interferons Non Confidential Presentation July 2007 20 Benefits VS Oral Agents Feature FTY 720 Cladribine BG 12 Laquinimod MN 166 Sponsor Novartis MerckSerono BiogenIdec Teva MediciNova Mechanism sphingosine 1 receptor agonist adenosine agonist, immunosuppressant fumaric acid deriv; NF k B inhibitor immuno modulator inhibits PDE IV, leukotrienes and NO synthesis; increases neuro trophic factors Dose 0.5, 1.25 or 5 mg/day low dose or high dose 120,360,720 mg/day 0.3 or 0.6 mg 60+ mg/day Indication Relapsing MS Relapsing MS Relapsing MS Relapsing MS Relapsing MS; delay disability progression?

By its early (within the first year) demonstrated decrease in brain volume loss, MN 166 may be providing such neuroprotection Currently available drugs have minimal effect on disability progression . A therapeutic approach that modulates inflammation, enhances neuron repair .and prevents neuron degeneration would be the most beneficial to patients over the long term.

Based on clinical and radiologic findings, MN 166 has the potential to modify disease progression by mitigating neuronal damage meeting the need for newer MS therapies sought by the MS scientific community. Proof of concept has been established and Phase III is targeted to begin in 08Q2 Non Confidential Presentation July 2007 13 Definition of next generation of MS treatment (abstracted from Neurology 68 (S3), 2007) Controlling inflammation is no longer sufficient Neuroprotection is a very important issue in MS and drugs that may provide neuroprotection are going to be very well received by the Neurology community The MRI metric of number of active lesions is not the most relevant to long term disability progression There are newer MRI metrics (e.g., brain atrophy measures) that will better correlate with neuroprotection and disability progression.

( e.g. , MN 166, MN 221)*. Asset selection is based on: Development time and costs Ability to sell with small, focused sales force (50 100 reps) Market potential pending completion of clinical trials and FDA approval Non Confidential Presentation July 2007 11 MN 166 (Multiple Sclerosis) Source Kyorin Pharmaceutical (2004) Mechanism Neuroprotective + Anti inflammatory Advantages Oral treatment for MS 17 year safety history in Japan (asthma, stroke) New U.S. use patent Clinical Status Positive Phase II results from one year treatment Milestones Full Phase II results anticipated 08Q1 Initiate Phase III as early as 08Q2 Commercial Strategy MNOV to commercialize in U.S. *pending FDA approval Non Confidential Presentation July 2007 12 MN 166: Next Generation Treatment for Multiple Sclerosis In an oral delivery form, MN 166 provides a high degree of safety with a broader ( neuroprotection + anti inflammatory ) efficacy profile than interferons.

You should not rely unduly on these forward looking statements, which speak only as of the date hereof. We undertake no obligation to update publicly or revise any forward looking statements discussed in this presentation. Safe Harbor Statement Non Confidential Presentation July 2007 3 Corporate Overview U.S. based pharmaceutical company developing and commercializing small molecule therapeutics sourced primarily from Japan Special relationships provide unique access to untapped source of novel therapeutics Broad, deep and advanced development pipeline with key market advantages Multiple opportunities for asset realization Lead commercial candidates MN 221 (Phase II) and MN 166 (Phase II) targeted Seasoned management team with global pharmaceutical experience Non Confidential Presentation July 2007 4 Innovative Business Model IN LICENSE high value, differentiated small molecule product candidates from mid sized Japanese pharmaceutical companies ADVANCE through proof of concept Phase II/III clinical trials MONETIZE assets at key value inflection points COMMERCIALIZE certain product candidates for maximum ROI Drug Development Research Late Preclinical Phase I Phase II Phase III Sales/ Marketing Value Inflection: $$$$$ Commercialize: $$$$$$$$$$ In License: $ Non Confidential Presentation July 2007 5 IN LICENSE Seek Differentiated small molecules (NCEs) in late preclinical to early Phase II stage that: Fill unmet medical needs Offer competitive market advantages Possess significant market potential Source Mid sized Japanese pharma ( e.g. , Kyorin, Kissei, Mitsubishi, Meiji) Special relationships provide unique access to untapped source Long history of successful small molecule products Large, detailed data packages Strong IP Non Confidential Presentation July 2007 6 Commercially Attractive Pipeline Product candidate (indication) Preclinical Phase 1 MN 166 (Multiple sclerosis) MN 305 (Anxiety Disorders/Insomnia) MN 221 (Status Asthmaticus) MN 001 (Bronchial asthma) MN 001 (Interstitial cystitis) MN 029 (Solid tumors) Phase 2 Phase 3 MN 246 (Urinary incontinence) Approval MN 221 (Preterm labor) MN 447 MN 462 (Thrombosis) Non Confidential Presentation July 2007 7 ADVANCE Advance to next value inflection point (usually Phase II/III proof of concept) Cost effective development through tightly managed CROs Experience and expertise in U.S. and European drug development Successful advancement has brought new candidates into the portfolio and facilitates future in licensing (renewable business model) Non Confidential Presentation July 2007 8 MONETIZE At value inflection point: Take selected assets forward to commercialization* ( e.g. , MN 221) Out license to global or regional partner Form joint venture to develop asset(s) Royalty based financing Multiple Opportunities to Realize Asset Value *pending FDA approval Non Confidential Presentation July 2007 9 MN 001: Opportunity to Monetize Novel, oral control medication for asthma Positive Phase II proof of concept data Significant improvement in FEV1 Excellent safety profile Once a day formulation in development (expected 08Q2) New composition of matter patent (expiry 2023) Non Confidential Presentation July 2007 10 COMMERCIALIZE Commercialize selected product candidates in the U.S.

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, 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 our product candidates, the uncertainty of whether the results of clinical trials will be predictive of results in later stages of product development, the risk that regulatory authorities may find our filings incomplete or insufficient or otherwise unacceptable or that approval may be delayed or denied, our reliance on third parties and the timing, cost and design of future clinical trials and research activities, the timing of our expected filings with the FDA, the failure to execute strategic plans or strategies successfully, our collaborations with third parties, and the other risks and uncertainties described in our filings with the Securities and Exchange Commission, including our annual report for the year ended December 31, 2006 and our subsequent periodic reports on Forms 10 Q and 8 K.

These forward looking statements include, but are not limited to, statements regarding our strategies and objectives, our plans for the development and commercialization of our product candidates, including development programs and clinical trials, our industry, our financial condition, liquidity and capital resources, the efficacy and potential benefits of our product candidates and other statements that are not historical facts.

MediciNova, Inc. 2007 Accelerating the global development and commercialization of innovative pharmaceutical products Accelerating the global development and commercialization of innovative pharmaceutical products Exhibit 99.1 Non Confidential Presentation July 2007 2 This presentation contains forward looking statements that involve risks and uncertainties.