Background There have been very few population-based studies of the prevalence of psychiatric disorders among children and adolescents with and without intellectual disability (ID). Methods Secondary analysis of the 1999 Office for National Statistics survey of the Mental Health of Children and Adolescents in Great Britain was performed. This survey collected information on a multistage, stratified, random sample of 10 438 children between 5 and 15 years of age across 475 postcode sectors in England, Scotland and Wales. Results The prevalence of any diagnosed ICD-10 disorder, conduct disorder, anxiety disorder, hyperkinesis and pervasive developmental disorders were significantly greater among children with ID than among their non-ID peers. There were no statistically significant differences between children with and without ID with regard to the prevalence of depressive disorders, eating disorders or psychosis. Factors associated with an increased risk of psychopathology among children and adolescents with ID included age, gender, social deprivation, family composition, number of potentially stressful life events, the mental health of the child's primary carer, family functioning and child management practices. Conclusions Children and adolescents with ID are at significantly increased risk of certain forms of psychiatric disorder. Careful consideration of the social and economic adversity facing such families will be necessary to ensure that support services are responsive to both the needs of child as well as the needs of the family in which they are living