Background: Data on the health of adolescents with intellectual disability are scarce. This study describes carer-reported symptoms, chronic illnesses, level of functioning, and behaviour among Australian adolescents with intellectual disability. We compare students attending mainstream and special schools. Methods: Cross-sectional questionnaire data were obtained from a cohort of 592 adolescents (10–21 years) with intellectual disability attending school and living in South-East Queensland, Australia, in May 2007. We analysed data from a subset (176) who completed a health check before visiting their general practitioners. Results: Adolescents had significant health needs, and those in special education schools had worse health than those from mainstream schools. There was a discrepancy between the prevalence of significant psychopathology detected via the short form Developmental Behaviour Checklist (DBC-P24) and psychiatric conditions reported by carers. Conclusions: Given the significant health needs of this population, carefully designed and targeted programs, potentially including medical visits to these schools, are needed.