OBJECTIVE: To determine the influence of gender, apolipoprotein E phenotypes, and diet on the interindividual variances in serum lipid and lipoprotein concentrations in children at 7 and 13 months of age. STUDY DESIGN: Prospective randomized intervention trial. Half of 1062 families with 7-month-old infants received dietary and lifestyle counseling aimed at partially replacing saturated fat with mono- and polyunsaturated fat and reducing exposure to other known atherosclerosis risk factors. This study comprises all trial children who at 8 months of age received, in addition to solid food, only breast milk or only formula (N = 553). Forward stepwise multiple regression analysis was used in the evaluation of the contributions of gender, apolipoprotein E phenotype, and diet. RESULTS: Apolipoprotein E phenotypes, gender, and milk type provided independent information concerning serum lipid values at 7 and 13 months of age (three-way ANOVA, p < 0.01). At 7 months, milk type was the most significant predictor of total, non-high-density lipoprotein and high-density lipoprotein cholesterol and apolipoprotein B and A1 concentrations. At 13 months when the effects of gender (5%) and apolipoprotein E type (5%) were excluded, diet predicted only 2% of the variance in serum cholesterol concentration. The apolipoprotein E type predicted 8% of the variance in non-high-density lipoprotein cholesterol concentration and 7% of the variance in apolipoprotein B concentration (p < 0.001), together explaining only 3% of the variance in serum high-density lipoprotein cholesterol and apolipoprotein A1 concentrations. CONCLUSIONS: At 7 months of age diet is an important predictor of serum lipid and lipoprotein concentrations. At the age of 13 months the apolipoprotein E phenotype significantly predicts the concentrations of serum non-high-density lipoprotein cholesterol and apolipoprotein B. However, at both ages apolipoprotein E phenotype, gender, and diet together explain only from 1.4% to 15.5% of the variance in serum lipids and apolipoproteins, suggesting that other, presumably genetic, factors are major determinants.