The São Paulo Megacity Mental Health Survey is a population-based cross-sectional survey of psychiatric morbidity, assessing a probabilistic sample of household residents in the São Paulo Metropolitan Area, aged 18 years and over. Respondents were selected from a stratified multistage clustered area probability sample of households, covering all 39 municipalities, without replacement. Respondents were assessed using the World Mental Health Survey version of the World Health Organization Composite International Diagnostic Interview (WMH-CIDI), which was translated and adapted into the Brazilian-Portuguese language. Data was collected between May 2005 and April 2007 by trained lay interviewers. The World Mental Health Survey version of the Composite International Diagnostic Interview comprises clinical and non-clinical sections, arranged as Part I and Part II, producing diagnoses according to the Diagnostic and Statistical Manual of Mental Disorders - Fourth Edition, and the International Classification of Diseases - 10th Revision. Mood, anxiety, impulse-control and substance use disorders, and suicide-related behavior, considered core disorders, as well as socio-demographic information, were assessed in all respondents. Non-clinical modules and non-core clinical sections (obsessive-compulsive disorder, post-traumatic stress disorder, gambling, eating disorders, neurasthenia, pre-menstrual disorders, psychotic symptoms and personality traits) were assessed in a sub-sample (2,942 respondents), composed by all respondents with at least one core disorder and a 25% random sample of those who were non-cases. A total of 5,037 individuals were interviewed, with a global response rate of 81.3%. Saliva samples were collected from 1,801 respondents, with DNA extracted stored pending further investigations.