Objective: Although differences in body composition parameters among African American (AA), Hispanic American (HA) and European American (EA) children are well documented, the factors underlying these differences are not completely understood. Environmental and genetic contributors have been evaluated as contributors to observed differences. This study evaluated the extent to which African or European ancestral genetic background influenced body composition and fat distribution in 301 peripubertal AA (n=107), HA (n=79) and EA (n=115) children aged 7-12.Design:Estimates of African admixture (AFADM) and European admixture (EUADM) were obtained for every subject using 142 ancestry informative DNA markers. Dual energy X-ray absorptiometry and computed tomography scanning were used to determine body composition and abdominal fat distribution, respectively. Multiple regression models were conducted to evaluate the contribution of admixture estimates to body composition and fat distribution. Results: Greater AFADM was associated with lower fat mass (P≥0.0163), lower total abdominal adipose tissue (P≥0.0006), lower intra-abdominal adipose tissue (P≥0.0035), lower subcutaneous abdominal adipose tissue (P≥0.0115) and higher bone mineral content (BMC) (P≥0.0253), after adjusting for socio-economic status, sex, age, height, race/ethnicity and pubertal status. Greater EUADM was associated with lower lean mass (LM) (P≥0.0056). Conclusion: These results demonstrate that ancestral genetic background contributes to racial/ethnic differences in body composition above and beyond the effects of racial/ethnic classification and suggest a genetic contribution to total body fat accumulation, abdominal adiposity, LM and BMC. © 2011 Macmillan Publishers Limited All rights reserved.