We describe the lipoprotein and apolipoprotein profiles and their relationship to cardiovascular risk factors in Australian Aboriginal children. This cross-sectional study within a longitudinal birth cohort study involved Australian Aboriginal children born between 1987 and 1990 and re-examined between 1998 and 2001. Height, weight, blood pressure, waist circumference, body fat percentage, cholesterol, triglycerides, HDL-c, LDL-c, apolipoprotein B and A1 were measured. Mean age was 11.4 years (52% male). Mean cholesterol, triglyceride, HDL-c and LDL-c did not differ from reference data. Measures of obesity, blood pressure and prevalence of the metabolic syndrome did not differ in those children with lipoproteins in the upper quartile of the cohort (lower quartile for HDL-c). Boys with an Apo-B/A1 ratio in the upper quartile of the cohort had higher BMI z-score, waist z-score, % body fat, diastolic blood pressure and frequency of the metabolic syndrome (p<0.05). In girls, waist circumference, % body fat and the prevalence of the metabolic syndrome was higher in those with an Apo-B/A1 ratio in the upper quartile (p<0.05).The Apo-B/A1 ratio may be useful to identify cardiovascular risk in Australian Aboriginal children and is suited to clinical practice as the assays are standardised, accurate, automated and a fasting sample is not required.