Background Few studies in Latin America have explored mental disorder among young offenders, or variables associated with it. Aims Our aim was to test for associations between childhood adversity or substance misuse and psychiatric disorders among young offenders. Methods Sentenced adolescent offenders were recruited from young offenders' institutions or community centres provided by the Chilean National Service for Minors. Psychiatric disorders were assessed using the Mini International Neuropsychiatric Interview, conducted by trained psychologists. A trained sociologist used an ad hoc interview to collect information about childhood experiences, including parenting, trauma, education and substance misuse. Multivariable logistic regressions were used to analyse data. Results The most prevalent psychiatric disorders among the 935 participants were marijuana dependence disorder, major depressive disorder, and anxiety disorders. Substance use disorders were less frequent among young offenders who were serving their sentence in young offenders' institutions than among those serving in community centres and more frequent among those who started to use marijuana at an earlier age. Among other variables, childhood maltreatment was related to major depressive disorder, and maternal death to anxiety disorders. Higher educational status was related to a lower frequency of depressive and anxiety disorders. Conclusions Our findings suggest that greater efforts must be made to identify vulnerable young people much earlier. Few of these young offenders with mental health problems had been well adjusted in health, education or socially before this period of detention. © 2017 The Authors. Criminal Behaviour and Mental Health Published by John Wiley & Sons Ltd