Individuals with co-occurring disorders are characterized by significant heterogeneity, and several different combinations of commonly occurring mental health and substance use disorders are described in the Diagnostic and Statistical Manual of Mental Disorders. Each combination of co-occurring disorders is characterized by differences in the following areas: prevalence rates, primary drugs of choice, etiology and history, history of institutionalization, symptoms, functional impairment, level of social support, course of the disorders and treatment, prior involvement with the criminal justice system, history of aggressive and violent behavior, and ability to function independently in institutional or community settings. Individuals in the criminal justice system who are at greatest risk for co- occurring disorders are considered, as well as the effects of co- occurring disorders on treatment and the importance of screening, diagnosis, and assessment. The definition and assessment of mental health and substance use disorders are discussed, and the importance of collecting adequate information to screen for co- occurring disorders is stressed. Key clinical issues associated with co-occurring disorders are addressed, screening and diagnostic instruments for co-occurring disorders are identified, and guidelines on the assessment of co-occurring disorders are offered. The authors conclude a coordinated system of screening, diagnosis, and assessment for mental health and substance use disorders should be established in all criminal justice settings. Supplemental information on the co-occurrence of specific mental and substance use disorders is appended. 173 references