OBJECTIVE: The aim of this study was to determine the characteristics and referral pattern of children and adolescents with mental health problems, substance misuse and comorbidity presenting to the emergency department (ED) of a large public hospital. METHOD: A file audit of the ED information system was conducted over a 12 month period. Outcome measures included age, gender, diagnostic presentation, assessment, referral and disposal. RESULTS: Forty-four substance misuse, 128 mental health and 82 comorbidity presentations were identified; 80% required treatment within 30 minutes. Few substance misuse cases were seen by mental health services and no substance misuse cases were referred for mental health service assessment. All mental health and comorbidity cases were seen by mental health services; 41% were referred to outpatient and 18% to inpatient services. Those with mental health problems displayed high levels of self-mutilation, and those with comorbidity displayed high levels of self-mutilation and substance misuse. Alcohol use was common in the substance misuse group, and over the counter or prescription medications were abused by the mental health and comorbidity groups. CONCLUSIONS: This age group places a high demand on the ED. All children and adolescents with recognized mental health symptoms were seen by mental health services, but those with substance misuse were not. Given the long-term problems associated with substance misuse, this is a missed opportunity for intervention.