OBJECTIVE: The purpose of the present study was to determine the impact of body fat mass and fat distribution on serum lipids, lipoproteins and apolipoproteins in African-American and Caucasian-American prepubertal children. SUBJECTS: Study participants included 62 African-American children (age 8.3 ± 1.4y; body mass 37.3 ± 13.6 kg; height 133 ± 11 cm) and 39 Caucasian children (age 8.6 ± 1.2y; body mass 34.1 ± 11.0 kg; height 131 ± 9cm). METHODS: Venous blood samples were obtained after a 12 h overnight fast and serum was analyzed for total cholesterol (TC), high-density lipoprotein-cholesterol (HDL-C), triacylglycerol CRAG), apolipoprotein A-I (ApoA-I), apolipoprotein B (ApoB) and lipoprotein (a) (Lp(a)) concentrations. Body composition and body fat distribution were measured by dual-energy X-ray absorptiometry and computed tomography, respectively. RESULTS: African-American children had lower TAG (46 ± 20 vs 61 ± 32 mg/dl, P = 0.015) and higher Lp(a) (34 ± 25 vs 17 ± 28 mg/dl, P = 0.001) and HDL-C (44 ± 11 vs 39 ± 8 mg/dl, P = 0.041). There were no ethnic differences in TC, ApoA-I and ApoB (P = 0.535, P = 0.218, P = 0.418, respectively). The ethnic difference in TAG and Lp(a) was not explained by total fat or abdominal fat. The ethnic difference in HDL-C was explained by visceral fat and TAG. CONCLUSION: In prepubertal children, neither body fat nor fat distribution explain the ethnic difference in TAG or Lp(a), but visceral fat and TAG may contribute to differences in HDL-C.