Abstract-The autoimmune MRL/lpr mouse strain, a model for systemic lupus erythematosus, exhibited an unusual plasma lipoprotein profile, suggesting a possible interaction of autoimmune disease and lipoprotein metabolism.In an effort to examine the genetic basis of such interactions, and to study their relationship to atherogenesis, we performed a quantitative trait locus analysis using a total of 272 (MRL/lprϫBALB/cJ) second generation (F2) intercross mice. These mice were examined for levels of total plasma cholesterol, HDL cholesterol, VLDL and LDL cholesterol, unesterified cholesterol, autoantibodies, and aortic fatty streak lesions. Key Words: linkage analysis Ⅲ antibodies, antinuclear Ⅲ genes Ⅲ lupus erythematosus, systemic Ⅲ HDL P lasma lipoprotein levels are an important determinant of atherosclerosis, the major cause of coronary artery disease (CAD) and stroke. High levels of LDL and VLDL are strongly associated with increased incidence of CAD, whereas HDL has a protective effect. 1-4 Although a number of mendelian disorders contributing to lipoprotein metabolism, such as those of the LDL receptor in familial hypercholesterolemia and cholesterol ester transfer protein deficiency in hyperalphalipoproteinemia, have been elucidated, 1,5,6 they explain only a small fraction of the population variance of plasma lipoprotein levels. As yet, relatively little is known of the genetic factors contributing to common, complex genetic variations. Studies of such variations in humans are complicated by dietary influences and genetic heterogeneity. Animal models have significant advantages for the analysis of complex traits 7-11 ; in particular, planned breeding can be performed and the environment can be controlled. The mouse, the most useful mammal for genetic studies, has been developed as a model for the analysis of lipoprotein metabolism and other traits relevant to atherosclerosis. In previous studies in our laboratory, we have identified several quantitative-trait loci (QTL) for lipoprotein metabolism in mice, and some of the underlying genes were elucidated using a positional candidate gene strategy. 10,11