Hypertriglyceridemia is frequently associated with obesity. In the general Caucasian population, an association of the uncommon S2 allele of a DNA polymorphism of the apolipoprotein (apo) A-I/C-III/A-IV gene cluster with hypertriglyceridemia has been reported. To assess the risk of hypertriglyceridemia associated with the S2 allele in obesity, lipid status and apo A-I/C-III/A-IV genotypes were studied in 90 unrelated Caucasian obese subjects. Age, body mass index, percentage body fat and waist-hip ratio were comparable between genotypes. The frequency of S1/S2 genotype was 35% in the hypertriglyceridemic group versus 11.4% in the normotriglyceridemic group (P < 0.05). The odds ratio of hypertriglyceridemia was 3.7 for obese subjects with the S2 allele and 26.7% of hypertriglyceridemias could be attributed to the S2 allele. Women with the S1/S2 genotype had also significantly higher VLDL- and LDL-cholesterol concentrations. These results suggest that the S2 allele modulates the effects of obesity on lipoproteins and increases the risk of hypertriglyceridemia when obese.