Genetic polymorphism of apolipoprotein E (apoE) and the Xbal restriction-fragment-length polymorphisms (RFLP) of the gene for apolipoprotein B (apoB) have both been shown to be associated with plasma lipid concentration. We studied the combined effect of these gene polymorphisms on serum cholesterol concentrations in 300 subjects aged nine to 18 years. In three way ANOVA, there was a statistically significant interaction between the effects of apoE phenotype and gender on serum cholesterol (P = 0.009). Therefore, males and females were analysed separately by two way ANOVA: there was no interaction between the effects of apoE phenotype and apoB Xbal polymorphism in either gender. In females, there were independent effects of both the apoE phenotype (P = 0.020) and the apoB Xbal genotype (P = 0.037) on serum cholesterol, but in males these effects were not statistically significant. These data suggest that variations at the apolipoprotein B and E gene locus play a role in the determination of serum cholesterol concentration in young female Finns.