Coronary heart disease is a complex genetic disease with many genes involved, environmental influences, and important gene-environment interactions. This review discusses the genetic basis of the principal lipoprotein abnormalities associated with coronary heart disease susceptibility in the general population. Individual sections discuss genes regulating LDL cholesterol, HDL cholesterol, and triglyceride levels. A section is included on the effects of the common apo E genetic variation on lipoprotein levels, as well as sections on the genetic regulation of lipoprotein(a) levels, genes regulating the inverse relationship between triglyceride-rich lipoproteins and HDL cholesterol levels, and our current understanding of the genetic basis of familial combined hyperlipidemia. It is clear that the field has progressed, with early studies focused mainly on the association of candidate gene RFLPs with phenotypes, later studies of candidate genes in both parametric and nonparametric linkage studies, and now more and more studies combining linkage analysis with genome scans to identify new loci that influence lipoprotein phenotypes. The future should provide us with the capability to perform reasonable genetic profiling for lipoprotein abnormalities associated with coronary heart disease susceptibility.