Objective-We sought to identify novel atherosclerosis-modifying loci and their potential functional links in a genome-wide approach using cosegregation analysis of atherosclerosis and related intermediate phenotypes in mice. Methods and Results-We carried out an F2 intercross between atherosclerosis-susceptible C57BL/6 mice and atherosclerosis-resistant BALB/cByJ mice on the low-density lipoprotein receptor Ϫ/Ϫ background to examine the genetic basis for their differences in atherosclerosis susceptibility. Atherosclerotic lesion size and a comprehensive panel of 61 atherosclerosis-related phenotypes, including plasma levels of lipids, cytokines, and chemokines were measured in 376 F2 mice. Quantitative trait locus mapping revealed a novel significant locus (logarithm of odds, 6.18) for atherosclerosis on proximal mouse chromosome (Chr) 2 (Ath39), which was associated with major variations in lesion size (14%). Plasma very-low-density lipoprotein-cholesterol, high-density lipoprotein-cholesterol, lanosterol, and phytosterol levels cosegregated with atherosclerosis at this locus. Moreover, these lipid traits showed significant correlations with lesion size, suggesting that they share the same underlying genetic factor. We also describe a second male-specific locus on Chr 8 (Ath40) where atherosclerosis and lipids cosegregated. Conclusion-Our study revealed new loci for atherosclerosis susceptibility on mouse Chr 2 and 8, which might exert their effects on lesion size via plasma lipid levels. espite successes in treatment of risk factors, atherosclerotic cardiovascular disease remains the major cause of morbidity and mortality in much of the world today. 1 Susceptibility to atherosclerosis is a complex genetic trait, determined by multiple genetic and environmental factors. Heritability estimates demonstrated that up to 50% of the disease susceptibility is attributable to genetics, 2 making genetic factors a major contributor to pathogenesis. Recently, genome-wide association studies in humans have led to the identification of several novel loci of atherosclerotic cardiovascular disease. 3 Genetic differences in susceptibility to atherosclerosis have also been described between several inbred mouse strains 4 -6 and used in unbiased genome-wide linkage studies to map genomic regions and atherosclerosismodulating genes. More than 30 quantitative trait loci (QTLs) for atherosclerosis have been identified by linkage mapping in mice, many of which exhibit corresponding loci in homologous regions in humans. 7 Because it is likely that the same orthologous genes are responsible for concordant loci in mice and humans, identifying atherosclerosis genes in mice can provide important new insights relevant to human pathology. This can be exemplified by the identification of Alox5 (mice)/ALOX5AP (human) and Tnfsf4 (ox40L) as new atherosclerosis-modulating genes in mice and humans. 8 -10 The fact that most recent mouse linkage studies were able to identify new genomic regions for atherosclerosis suggests that our current inven...