Rates of overweight and obesity in Australian children have increased significantly during the past twenty years, with Aboriginal children disproportionately affected. Unlike BMI, waist-to-height (WtHR) is a relatively constant anthropometric index of central intra-abdominal adiposity in children across age, sex and socio-demographic groups. In the current study, we aimed to determine risk factors for central obesity in Aboriginal and non-Aboriginal children, and whether Aboriginal children are at increased risk of central obesity after accounting for socio-demographic factors. Children were enrolled into the ARDAC study, a prospective cohort study, from across 15 different screening centres involving 122 primary schools and 213 high schools across urban, regional and remote NSW from Jan 2002 to Dec 2012. WtHR was calculated as waist circumference divided by height. Central obesity was defined as WtHR greater or equal to 0.5 (WtHR ≥ 0.5). Socioeconomic status, area of residence and birth weight were also recorded at study enrolment. We applied logistic regression to assess if Aboriginal children were at higher risk of central obesity, with separate models created for girls and boys. WtHR was measured in 2158 children (58% Aboriginal; 50% boys, mean age 14.1±1.8 [SD] years). Aboriginal girls were more likely than non-Aboriginal girls to have central obesity (31.5%, 95% CI 27.8-35.1% versus 17.0%, 95% CI 13.5-20.5%), and had a two-fold increased risk of central obesity after adjusting for age and remoteness (OR 2.26, 95% CI 1.65-3.10). Aboriginal boys may be at small but increased risk of central obesity (22.9%, 95% CI 19.6-26.3% versus 18.2%, 95% CI 14.7-21.8%, P = 0.06; adjusted OR 1.30, 95% CI 0.96-1.76). Aboriginal girls were substantially more likely than non-Aboriginal girls to have central intra-abdominal obesity, as measured by WtHR ≥ 0.5. Intervention programs should recognise that childhood is a critical time for prevention of obesity, particularly for the Aboriginal community.