The impact of the common alleles at structural loci coding for apolipoprotein (apos) A-IV, E, and H on 12 quantitative risk factors for cardiovascular disease (apos A-I, A-II, B, C-II, C-III, and E; total cholesterol; triglycerides; high density lipoprotein cholesterol; systolic blood pressure; diastolic blood pressure; and red blood cell sodium-lithium countertransport) was estimated in 453 unrelated individuals (227 men and 226 women) aged 26-63 years from the Rochester Family Heart Study, who were not using medications affecting lipid levels or blood pressure. Each risk factor was adjusted for concomitants (assay date, age, age, squared, height, weight and smoking status) before the genotypic effects on mean levels and variances were estimated. Allele frequencies were the same in men and women and were similar to those observed in other studies of US Caucasians. There were very different gender-specific estimates of the relative contribution of concomitants, measured genetic effects, and residual unexplained effects to the interindividual variation of particular traits. Allelic variation in apo E had effects on the greatest number of traits, namely apo E, apo B, apo C-II, and total cholesterol. An effect on triglycerides was dependent on the inclusion of hypertriglyceridemic subjects. Allelic effects of apo A-IV and apo H were much less than those estimated for the apo E polymorphism. A possible role for apo H in high density lipoprotein metabolism is suggested. This study indicates that variation in many genes may influence variation in a particular trait and that a particular gene may have pleiotropic effects on several traits.