Background: Adult Aboriginal Australians have 1.5-fold higher risk of obesity, but the trajectory of body mass index (BMI) through childhood and adolescence and the contribution of socio-economic factors remain unclear. Our objective was to determine the changes in BMI in Australian Aboriginal children relative to non-Aboriginal children as they move through adolescence into young adulthood, and to identify risk factors for higher BMI. Methods: A prospective cohort study of Aboriginal and non-Aboriginal school children commenced in 2002 across 15 different screening areas across urban, regional and remote New South Wales, Australia. Socio-economic status was recorded at study enrolment and participants' BMI was measured every 2 years. We fitted a series of mixed linear regression models adjusting for age, birth weight and socio-economic status for boys and girls. Results: In all, 3418 (1949 Aboriginal) participants were screened over a total of 11 387 participant years of follow-up. The prevalence of obesity was higher among Aboriginal children from mean age 11 years at baseline (11.6 vs 7.6%) to 16 years at 8 years follow-up (18.6 vs 12.3%). The mean BMI increased with age and was significantly higher among Aboriginal girls compared with non-Aboriginal girls (P<0.01). Girls born of low birth weight had a lower BMI than girls born of normal birth weight (P<0.001). Socio-economic status and low birth weight had a differential effect on BMI for Aboriginal boys compared with non-Aboriginal boys (P for interaction=0.01). Aboriginal boys of highest socio-economic status, unlike those of lower socio-economic status, had a higher BMI compared with non-Aboriginal boys. Non-Aboriginal boys of low birth weight were heavier than Aboriginal boys. Conclusions: Socio-economic status and birth weight have differential effects on BMI among Aboriginal boys, and Aboriginal girls had a higher mean BMI than non-Aboriginal girls through childhood and adolescence. Intervention programs need to recognise the differential risk for obesity for Aboriginal and non-Aboriginal boys and girls to maximise their impact.