The effects of dietary intervention, sex, and apolipoprotein E phenotype on tracking of serum lipid values in young children have remained poorly characterized. We investigated these associations in 1062 infants who were randomized into control and intervention groups (n=522 and n=540, respectively) at age 7 months; the intervention group received counseling aimed at maintaining a low-saturated fat, low-cholesterol diet. In 519 children in the control (n=254) and intervention (n=265) groups, serum lipid values were studied annually between 13 months and 5 years of age. In all children, tracking was strongest for the ratio of high density lipoprotein (HDL) cholesterol to total cholesterol; when a 13-month-old child belonged to the lowest quartile of the distribution, the odds ratio for belonging to the same quartile at older ages was 39.0 (95% CI 23.1 to 66.0). Dietary intervention did not influence the tracking of serum lipids. Tracking of HDL cholesterol was stronger in the boys than in the girls (P=0.018). Tracking of non-HDL cholesterol and apolipoprotein B in the children with phenotypes E2/3 or E3/3 was stronger than that in the other children (P=0.031 and P=0.014, respectively). In conclusion, the apolipoprotein E phenotype strongly influences tracking of non-HDL cholesterol and apolipoprotein B values in early childhood, whereas dietary intervention had no effect on tracking of any of the lipids. A child's sex influenced tracking only of HDL cholesterol, with boys showing stronger tracking.