Aims: Both substance use and mental illness commonly onset during adolescence or young adulthood, and rates of substance use in young people with mental illness are disproportionately high. This baseline data paper from a clinical trial testing an integrated early intervention for substance use and mental health problems aims to 1) describe the characteristics of participants enrolled; and 2) compare young people with a current and without a lifetime diagnosis of Substance Use Disorder (SUD) in terms of psychiatric symptoms, functioning, and substance use. Methods: Seventy-nine participants aged 12-25 years with high prevalence mental illness (e.g., depression, anxiety) and substance use seeking mental healthcare were recruited from headspace primary mental health centres in North-Western Melbourne. At baseline, they completed self-report and interview measures of psychiatric diagnoses and symptoms, functioning, and substance use. We compared those with a current (n=51) and without a lifetime (n=21) SUD on these measures. Results: Youth with an SUD endorsed more severe depressive and anxiety symptoms, and lower quality of life and role functioning than those who used substances without a lifetime SUD. They also had more alcohol-related problems and higher frequency cannabis use, and higher risk scores for alcohol, tobacco, cannabis, cocaine, amphetamine-type stimulants, and hallucinogen use. There were no group differences in social and occupational functioning or subjectively-rated sleep quality. Conclusions: Findings highlight the need for early identification and integrated care models within youth mental health services to address the high prevalence and impact of problematic substance use, potentially reducing adverse effects of co-occurring SUD and mental illness on youth development and functioning.