Background: While research indicates elevated behavioural and emotional problems in children with autism spectrum disorders (ASD) and decreased well-being in their parents, studies do not typically separate out the contribution of ASD from that of associated intellectual disabilities (ID). We investigated child behavioural and emotional problems, and maternal mental health, among cases with and without ASD and ID in a large population-representative sample. Methods: Cross-sectional comparison of child behavioural and emotional problems and maternal mental health measures among 18,415 children (5 to 16 years old), of whom 47 had an ASD, 51 combined ASD with ID, 590 had only ID, and the remainder were the comparison group with no ASD or ID. Results: The prevalence of likely clinical levels of behavioural and emotional problems was highest among children with ASD (with and without ID). After controlling for age, gender, adversity, and maternal mental health, the presence of ASD and ID significantly and independently increased the odds for hyperactivity symptoms, conduct, and emotional problems. Emotional disorder was more prevalent in mothers of children with ASD (with or without ID). The presence of ASD, but not ID, significantly increased the odds for maternal emotional disorder. As has been found in previous research, positive maternal mental health was not affected by the presence of ASD or ID. Conclusions: ASD and ID are independent risk factors for behavioural and emotional problems. ASD (but not ID) is positively associated with maternal emotional disorder. Approaches to diagnosing hyperactivity and conduct problems in children with ASD may need to be reconsidered. (Contains 4 tables.)