To determine if the apolipoprotein B gene and the apolipoprotein A1-C3-A4 gene cluster were independent predictors of premature coronary disease, the relation between DNA polymeric sites within the two genes and coronary disease were investigated using cloned DNA fragments as molecular probes. To determine if apolipoprotein B and apolipoprotein A levels aggregated in families and to determine if hyperapo B and hypoalphalipoproteinemia segregated as Mendelian traits, genetic analysis was conducted in the 200 index cases and the 900 first degree relatives. Studies were also conducted on the linkages between hyperapo B and haplotypes of the apolipoprotein B gene, on hyperapo B and the Ag polymorphisms, and on hyperalphalipoproteinemia and haplotypes of the apolipoprotein A1-C3-A4 gene cluster.