The Italian preadolescent mental health project (PrISMA--Progetto Italiano Salute Mentale Adolescenti) is the first Italian study designed to estimate the prevalence of mental disorders in preadolescents (10-14 years old) living in urban areas, and to analyse the demographic and biological correlates of emotional and behavioural problems. This paper describes the rationale, methods and the analysis plan of the project. The design of the study used a two-stage sampling procedure, one screening stage of emotional and behavioural problems in a large sample of subjects attending public and private schools and a second stage of diagnostic assessment in a sample including all high scorers and a proportion of low scorers. In the screening stage, parents of preadolescents were asked to fill in the Child Behavior Checklist (CBCL), whereas in the second stage preadolescents and their parents were administered the Development and Well Being Assessment for the assessment of mental disorders together with the Strengths and Difficulties Questionnaire and two scales (C-GAS and HoNOSCA) designed to evaluate the functioning of the preadolescent in different areas. Genetic samples were collected during the screening stage, after parents gave their informed written consent. The findings of this study are expected to allow an adequate planning of interventions for the prevention and the treatment of mental disorders in preadolescence as well as efficient health services.