High density lipoprotein (HDL) is the major plasma lipoprotein found in mice fed normal laboratory chow containing 4% fat. When female mice from some inbred strains, such as C57BL/6, are fed a high fat diet (1.25% cholesterol, 15% fat, and 0.5% cholic acid), the levels of HDL-cholesterol decrease by about 50%, and lipid staining lesions form in the aorta within 14 weeks. In other strains of mice, such as C3H and BALB/c, HDL-lipid levels decrease only slightly, and few or no aortic lesions are observed at 14 weeks. The genetic basis of these phenotypic differences was analyzed by using recombinant inbred strains derived from C57BL/6 and BALB/c and also from C57BL/6 and C3H/He. The two phenotypes segregated as simple Mendelian traits, and no recombination was observed between them. Thus, HDL-cholesterol levels and susceptibility to atherosclerosis appear to be determined by the same gene (or by two closely linked genetic factors that are a maximum of 1.7 centimorgans apart). This gene was named Ath-1, for atherosclerosis susceptibility, with alleles r for resistance and s for susceptibility. Ath-1 maps on chromosome 1 near Alp-2, a gene that determines the structure of apolipoprotein A-II, one of the two major proteins found in HDL. Ath-1 is clearly separable from Alp-2, and the distance between these genes is 6.0 centimorgans with a standard error of 4.2 centimorgans. In humans, levels of HDL are inherited and are inversely correlated with atherosclerosis; familial hyperalphalipoproteinemia is associated with high levels of HDL-cholesterol and decreased risk of heart disease. The human trait phenotypically resembles Ath-1 in the mouse.