Plasma non-HDL and HDL cholesterol levels are predictors of cardiovascular diseases. We carried out a genetic cross between two laboratory inbred mouse strains, C57BL/6J and CASA/Rk, to detect loci that control the plasma levels of non-HDL and HDL cholesterol. With regard to non-HDL cholesterol, chow-fed CASA/Rk males and females had 87% and 25% higher levels, respectively, than did C57BL/6Js. The levels of non-HDL cholesterol in F1s were similar to C57BL/ 6J. There was no strain difference in HDL cholesterol levels. An intercross between F1s was performed, and plasma non-HDL and HDL cholesterol was measured in 185 male and 184 female mice. In both male and female F2 mice, plasma non-HDL and HDL cholesterol levels were unimodally distributed; however, in both cases the values for females were significantly lower than for males. Therefore, linkage analysis was performed with sex as a covariate. Significant linkage for non-HDL cholesterol was found on chromosome 6 at 49 cM (LOD 5.17), chromosome 4 at 55 cM (LOD 4.22), and chromosome 8 at 7 cM (LOD 3.68). Significant linkage for HDL cholesterol was found on chromosome 9 at 14 cM (LOD 7.52) and chromosome 8 at 76 cM (LOD 4.69). A significant epistatic interaction involving loci on chromosomes 2 and 5 was also observed for non-HDL cholesterol. In summary, linkage analysis in these cross-identified novel loci confirmed previously identified loci in control of plasma non-HDL and HDL cholesterol and disclosed a novel interaction in controlling non-HDL cholesterol levels in the mouse. Plasma levels of non-HDL and HDL cholesterol have been shown to modulate the risk for cardiovascular diseases. Increased plasma levels of non-HDL cholesterol, especially in the form of LDL cholesterol, and decreased levels of HDL cholesterol are associated with increased risk for these diseases. Multiple studies have shown large individual-toindividual variation in plasma non-HDL and HDL cholesterol levels (1). The causes of this variation and the regulation of non-HDL and HDL cholesterol levels are only partially understood. Current understanding supports a complex interaction between environmental and genetic determinants. Yet, whereas much is known about the nature and effect of environmental factors including cigarette smoking, total dietary fat intake, types of dietary fatty acids, physical activity, and alcohol consumption, relatively little is known about the genetic basis of this variation. Data from twin and family studies have shown that ف 50% of the interindividual variability in LDL cholesterol and HDL cholesterol can be ascribed to genetic determinants; however, only some of the genes involved have so far been identified (2-6). Studies in pedigrees that segregate mutations in critical genes largely expand the understanding of the physiological and metabolic aspects of lipoprotein carriers of non-HDL and HDL cholesterol. Yet, although in some populations variants of these genes are sufficiently common to have an impact on non-HDL and HDL cholesterol levels, it is like...