Objective-Previously we found dramatic strain-dependent differences in a low flow model of vascular remodeling.Specifically, intima formation in the left common carotid artery was Ϸ30-fold greater in SJL compared to C3HeB/Fe (C3H/F) mice. We hypothesized that a few genes control intima formation in response to low flow. A C3H/F and SJL backcross resulted in broad range of N2 intima phenotypes. Methods and Results-Using genome-wide scan we identified two highly significant quantitative trait loci (QTLs) for intima, Im1 (intima modifier 1 locus) on chromosome 2 (Chr2; 77.6 cM, LODϭ6.4), and Im2 on Chr11 (17 cM, LODϭ5.3). One significant QTL Im3 was found on Chr18 (6 cM, LODϭ3.0), and two suggestive QTLs (LODϭ1.5 and 1.8) were identified on Chr7 and Chr17, respectively. Interestingly, the intima/media ratio trait mapped to the same QTLs as the intima trait. Haplotype mapping predicted 40 candidate genes. Six of these genes contained SNPs that differed between C3H/F and SJL. Conclusions-We have successfully mapped 3 QTLs (Im1, Im2, and Im3) that are associated with carotid intima formation in response to low blood flow. These results may be important in identifying genes that influence carotid intima-media thickening and predict cardiovascular disease in humans. Key Words: genetics Ⅲ intima Ⅲ low blood flow Ⅲ mouse Ⅲ SJL/J Ⅲ C3HeB/FeJ S ubclinical atherosclerosis is measured by intima-media thickening (IMT) in human carotid arteries, and carotid IMT is associated with increased cardiovascular risk. 1 Mechanisms responsible for formation and progression of carotid IMT are unknown. Importantly, about 40% of the variability in the carotid IMT depends on family history in humans. 2 A quantitative trait locus (QTL) has been identified for internal carotid IMT (LODϭ3.4) on human chromosome (chr) 12. 3 Intima has been proposed to be the "soil" for atherosclerosis, implying an important pathophysiologic role for this tissue. 4 Only one genetic analysis of intima hyperplasia in animals, the aortic response to balloon injury in an intercross between BN and SHR rats, has been published. 5 The authors identified several QTLs with the most significant intima hyperplasia QTL mapping to rat chr3. It is important to note that intima hyperplasia and atherosclerosis may be regulated by distinct genetic mechanisms in individual vascular beds as shown by a recent study in mouse that compared carotid versus aorta. 6 These results suggest that carotid IMT is a complex trait likely determined by multiple environmental and genetic factors. Nonetheless, it has been proposed that insights into mechanisms responsible for human carotid IMT may be identified by genetic studies in animal models of atherosclerosis. 7 Local hemodynamic factors (eg, shear stress) play an important role in carotid IMT. For example, carotid IMT is inversely related to carotid shear stress in healthy subjects: lower shear stress correlated with greater IMT values. 8 Moreover, lower shear stress also correlated with progression of coronary atherosclerosis. 9