This study examined the prevalence of substance use disorders (SUDs) among psychiatric patients aged 2-17 years in an electronic health records database (N=11,457) and determined patterns of comorbid diagnoses among patients with a SUD to inform emerging comparative effectiveness research (CER) efforts. DSM-IV diagnoses of all inpatients and outpatients at a large university-based hospital and its associated psychiatric clinics were systematically captured between 2000 and 2010: SUD, anxiety (AD), mood (MD), conduct (CD), attention deficit/hyperactivity (ADHD), personality (PD), adjustment, eating, impulse-control, psychotic, learning, mental retardation, and relational disorders. The prevalence of SUD in the 2-12-year age group (n=6210) was 1.6% and increased to 25% in the 13-17-year age group (n=5247). Cannabis diagnosis was the most prevalent SUD, accounting for more than 80% of all SUD cases. Among patients with a SUD (n=1423), children aged 2-12 years (95%) and females (75-100%) showed high rates of comorbidities; blacks were more likely than whites to be diagnosed with CD, impulse-control, and psychotic diagnoses, while whites had elevated odds of having AD, ADHD, MD, PD, relational, and eating diagnoses. Patients with a SUD used more inpatient treatment than patients without a SUD (43% vs. 21%); children, females, and blacks had elevated odds of inpatient psychiatric treatment. Collectively, results add clinical evidence on treatment needs and diagnostic patterns for understudied diagnoses.