To determine whether the risk of obesity-associated dyslipidemia in children is influenced by apolipoprotein E (apoE) polymorphism, we studied 137 obese, nongenetically related children aged 2.2-14.4 y (mean age, 9.9 +/- 3.1 y) with a weight-for-height excess of 43.7 +/- 17.9%. The apoE genotype was determined by studying specific DNA restriction patterns. Total cholesterol, HDL-cholesterol, and triglycerides were assayed in plasma before dietary treatment initiation. ApoE allele and phenotype distributions were comparable to those reported in the Caucasian population at large. Fifty-five children (41%) had elevated lipid levels. Compared with obese children with the epsilon3 or epsilon4 allele, those with the epsilon2 allele were more likely to have hypertriglyceridemia (19.5% versus 52.9%, p < 0.05) and had a higher mean triglyceride level: children with the epsilon4 allele were more likely to have a LDL-cholesterol elevation (34.7% versus 13.4%, p < 0.05). Our data demonstrate that, even in childhood, obesity is associated with a marked increase in the risk of lipoprotein abnormalities and that the latter are influenced by apoE polymorphism.