Apolipoprotein E (apoE) polymorphism is a genetic determinant of plasma lipid levels and of coronary heart disease risk. We determined apoE phenotypes and plasma lipid levels in 1564 subjects aged three to 18 years, living in five geographical areas of Finland in 1980. ApoE phenotyping was performed directly from plasma by isoelectric focusing and immunoblotting. The serum concentrations of total cholesterol, low density lipoprotein cholesterol and apolipoprotein B varied with apoE phenotype, and there were increases in all three variables (all P less than 0.001) of the order of E2/2 less than E3/2 less than E4/2 less than E3/3 less than E4/3 less than E4/4. These differences were present in all five areas. The mean levels of high density lipoprotein cholesterol, apolipoprotein A-I and triglyceride in the subjects did not differ between the apoE phenotypes or between their areas of residence. The apoE phenotype dependency of serum total and LDL cholesterol remained significant in all five areas during the six year follow-up from 1980 to 1986, when the mean level of serum total cholesterol fell by 5.8% in east (P less than 0.05) and by 4.4% in west Finland (P less than 0.05); the fall was steeper (P less than 0.01) in the east than the west. In all subjects, particularly those in west Finland, the size of the falls of serum total and LDL cholesterol concentrations depended on the apoE phenotype in the order of E3/2 less than E3/3 less than E4/3, but this effect was not seen in the east.(ABSTRACT TRUNCATED AT 250 WORDS)