Beginning in 1991, genetic variations in the gene products of A-IV, E, H, and APO(a) were determined by isoelectric focusing and SDS/immunoblotting; gene variations at the APOB, D, LDL receptor, hepatic lipase, lipoprotein lipase, and cholesteryl ester transfer protein were assayed by polymerase chain reaction protocols and by using cloned cDNA probes for restriction fragment length polymorphism (RFLP) analyses. Direct haplotype analyses of individuals employed a strategy using RFLP analysis combined with the use of allele specific oligonucleotides. Quantitative levels of apolipoprotein B, E, H and APO (a) were determined by immunological techniques. These data and prior data on levels of triglycerides, total cholesterol, HDL-, LDL- and HDL subfraction cholesterol were used in the quantitative genetic analysis. Estimates of the effect of alleles at each of the genetic loci on the quantitative apolipoprotein and lipoprotein levels employed the measured genotype approach. The effects of multisite haplotypes for RFLPs at various loci were estimated using the same methods. For common alleles in each system, estimates were made of the interaction of alleles at independent genetic loci in determining quantitative variables. Dietary information from the San Luis Valley population was used to estimate cholesterol intake identified. Allelic effects were estimated in these groups to gain insight into the effect of dietary cholesterol intake of the estimated allelic effects.