Genetic predisposition to cardiovascular risk may vary between different ethnic groups. We studied the effect of the FABP2 A54T polymorphism on biochemical and anthropometric cardiovascular risk factors in 114 obese Mexican subjects. The mean age of the patients studied was 36.8+/-13.3 years. Insulin resistance was present in 47%, hypercholesterolaemia in 49% and hypertriglyceridaemia in 45%. Frequency of the FABP2 genotype was 39% AA, 54.8% AT and 6.2% TT. The AT/TT group showed an increase in body mass index (34+/-7.1 vs. 31+/-4.8 kg/m2), waist circumference (101+/-15.7 vs. 96.5+/-15.8 cm), triglycerides (145+/-60.8 vs. 127+/-79.4 mg/dL; 1.64+/-0.67 vs. 1.43+/-0.89 mmol/L), total cholesterol (176+/-39.4 vs. 164+/-38.2 mg/dL; 4.55+/-1.02 vs. 4.24+/-0.99 mmol/L), LDL (121+/-24.2 vs. 111+/-25.9 mg/dL; 3.13+/-0.62 vs. 2.88+/-0.67 mmol/L) and VLDL (28.8+/-12.1 vs. 25.1+/-16.1 mg/dL; 0.74+/-0.31 vs. 0.64+/-0.41 mmol/L) compared to the AA group (p<0.05). The AT/TT group had greatly increased cardiovascular risk, with an OR of 7.56 (95% CI, 1.82-36.24; p<0.001) compared to the AA group. Our results suggest that A54T polymorphism of the FABP2 gene is associated with cardiovascular disease risk in obese subjects.