Autism is a neurodevelopmental disorder with a specific pattern of behavioural, communication and social problems. Additional mental health problems are often poorly understood and undetected. This study investigates the level and pattern of emotional and behavioural problems in young people with autism compared with children with intellectual disability (ID). Subjects were 381 young people with autism and a representative group of 581 Australian young people with ID aged 4–18 years. Parents/carers provided details of the emotional and behavioural problems of their child using the Developmental Behaviour Checklist (DBC-P). Young people with autism were found to suffer from significantly higher levels of psychopathology than young people with ID. The implications of this finding are discussed.