Genetic variants in the intestinal fatty acid-binding protein-2 (FABP2) gene have been associated with body composition phenotypes. We examined the association between the Ala54Thr variant in the FABP2 gene and levels of visceral (VAT) and sc (SAAT) abdominal fat in a group of 223 premenopausal African-American (n = 103) and Caucasian (n = 120) women. Subjects were genotyped for the marker. In addition, body composition was assessed by dual energy x-ray absorptiometry, and VAT was determined from a single computed tomography scan. The frequency of the Thr mutant allele did not differ significantly by ethnic group. After adjusting for total body fat, total abdominal adipose tissue (TAT) and SAAT were significantly lower in carriers of either one or two copies of the mutant Thr allele (P < 0.01). There was no association between total fat mass or VAT and the FABP2 polymorphism. Separate analyses by ethnic group showed that the association between the polymorphism and TAT and SAAT was observed in Caucasian (P < 0.01), but not in African-American (not significant), women. We conclude that women carriers of the FABP2 Thr allele have lower TAT and SAAT than noncarriers of the mutation. This association is present in Caucasian, but not in African-American, women.