BACKGROUND: The aim of this study is to estimate the lifetime and 12-month prevalence, severity and treatment of Diagnostic and Statistical Manual of Mental Disorders fourth edition (DSM-IV) mental disorders in Japan based on the final data set of the World Mental Health Japan Survey conducted in 2002-2006. METHODS: Face-to-face household interviews of 4130 respondents who were randomly selected from Japanese-speaking residents aged 20 years or older were conducted from 2002 to 2006 in 11 community populations in Japan (overall response rate, 56%). The World Mental Health version of the World Health Organization Composite International Diagnostic Interview (WMH-CIDI), a fully structured, lay administered psychiatric diagnostic interview, was used for diagnostic assessment. RESULTS: Lifetime/12-month prevalence of any DSM-IV common mental disorders in Japan was estimated to be 20.3/7.6%. Rank-order of four classes of mental disorders was anxiety disorders (8.1/4.9%), substance disorders (7.4/1.0%), mood disorders (6.5/2.3%) and impulse control disorders (2.0/0.7%). The most common individual disorders were alcohol abuse/dependence (7.3/0.9%), major depressive disorder (6.1/2.2%), specific phobia (3.4/2.3%) and generalized anxiety disorder (2.6/1.3%). While the lifetime prevalence of any mental disorder was greater for males and the middle-aged, the persistence (proportion of 12-month cases among lifetime cases) of any mental disorder was greater for females and younger respondents. Among those with any 12-month disorder, 15.3% were classified as severe, 44.1% moderate and 40.6% mild. Although a strong association between severity and service use was found, only 21.9% of respondents with any 12-month disorder sought treatment within the last 12 months; only 37.0% of severe cases received medical care. The mental health specialty sector was the most common resource used in Japan. Although the prevalence of mental disorders were quite low, mental disorders were the second most prevalent cause of severe role impairment among chronic physical and mental disorders. CONCLUSIONS: These results suggest lower prevalence of mental disorders in Japan than that in Western countries, although the general pattern of disorders, risk factors and unmet need for treatment were similar to those in other countries. Greater lifetime prevalence for males and greater persistence for females seems a unique feature of Japan, suggesting a cultural difference in gender-related etiology and course of disorders. The treatment rate in Japan was lower than that in most other high-income countries in WMH surveys.