The influence of apolipoprotein (apo) E polymorphism on the tracking of serum lipoprotein variables over a 6-year follow-up period was examined in 442 individuals aged 5-15 years at baseline. The apo E phenotype-specific differences in total cholesterol and low-density lipoprotein (LDL) cholesterol levels persisted in the study cohort at baseline and follow-up examinations. However, the correlations of baseline versus follow-up levels of total cholesterol and LDL cholesterol varied according to the apo E phenotype group, with the apo E2 group, carrying E2/2 and E3/2 phenotypes, showing highest correlation for these variables (r = 0.73 - 0.74) and the apo E4 carrying E3/4 and E4/4 phenotypes the lowest (r = 0.48 - 0.59). The tracking correlation for LDL cholesterol in the apo E2 group was different form that of the other phenotype groups (P < 0.05). In terms of persistence in ranks over time, of the individuals who were in the highest quartile of LDL cholesterol at baseline none of those in the apo E2 group, 63% of those in the apo E3 group carrying E3/3 phenotype, and 60% of those in the apo E4 group maintained this high rank at follow-up; corresponding values for persistence in ranking at the lowest quartile over time were 82% for the apo E2 group, 57% for the apo E3 group, and 33% for the apo E4 group. Further, in a multiple regression model, apo E phenotype was retained as a predictor variable only in the case of LDL cholesterol. Thus, apo E polymorphism influences not only the level of LDL cholesterol in childhood, but also its tracking at least over a 6-year period.