Despite longstanding recognition of disparities in Aboriginal and Torres Strait Islander child health, progress to reduce disparities is slow. To improve the capacity of policy makers to target resources, there is an urgent need for epidemiological studies providing prospective data on child health outcomes. We undertook a prospective population-based study of 344 Aboriginal and Torres Strait Islander children born in South Australia. Mothers and caregivers reported on child health conditions, use of health services and the social and familial context of the children. A total of 238 children with a mean age of 6.5 years participated in wave 2 follow-up. Overall, 62.7% of the children experienced one or more physical health conditions in the 12 months prior to wave 2 follow-up, 27.3% experienced a mental health condition and 24.8% experienced a developmental condition. The 12-month period prevalence of physical, developmental and mental health conditions was similar for children living in urban, regional and remote areas. While most children had had at least one visit with a general practitioner, some children experiencing physical, developmental and mental health conditions appear to be missing out on specialist and allied health care. Greater efforts by governments and policy makers are needed to strengthen outreach, recognition, referral and follow-up.