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Objective: We aimed at designing a cross sectional study to investigate the prevalence of psychiatric disorders in Iranian children and adolescents and to determine its relationship with social capital, life style, and parents' personality disorders. Method: This cross sectional study was a national project implemented in all provinces of Iran. In this community-based study, using ‎multistage cluster sampling method, we selected 1000 children and adolescents aged 6 to 18 years in each province. The total sample size reached to 31 000. ‎We randomly collected 170 blocks. Then, of each cluster head, we selected 6 cases including 3 cases of each gender in ‎different age groups (6- 9 years, 10- 14 years, and 15- 18 years). The clinical psychologists instructed the participants to complete the Persian version of Kiddie-Sads-‎Present and Lifetime Version (K-SADS-PL). In addition, demographic data (gender, age, education, parent education, and economic situation) and information on lifestyle, social capital, and parents' personality disorders were obtained from the participants. Discussion: This study presents a protocol for an epidemiological survey on the first estimates for the prevalence of psychiatric disorders in children and adolescents across the country. This large body of data, on a range of individual behavioural and emotional items and scores, allows us to compare the rates and patterns of deviance between urban and rural places of residence in 31 provinces of Iran with non Iranian samples surveyed with the same measures.