Abstract-The search for genes related to the cause of common complex disorders such as cardiovascular disease has been frustrating, partly because of the many factors known to contribute to cardiovascular disease and the potential "distance" of cardiovascular disease as a phenotype from genes and gene products. Linkage and association studies for phenotypes more proximal in the pathway from DNA sequence variation to overt clinical disease, such as ultrasound-defined carotid atherosclerosis, may potentially be more enlightening. Only one genetic variant previously reported to be associated with atherosclerosis or clinically evident cardiovascular disease, matrix metalloproteinase (MMP) 3, has shown consistently positive associations with carotid disease, although it has not been studied widely. Another, PON1 L55M, is weakly associated in subgroups only, and 2, ApoE and MTHFR, are equivocal. Genetic variants reported to be associated with clinical cardiovascular disease show weak or no relationship to carotid atherosclerosis. This may reflect the known inconsistency in associations of genetic variants with clinical cardiovascular disease itself. Alternatively, genetic determinants of ultrasound-defined carotid atherosclerosis may differ from those of clinically manifest cardiovascular disease and may require pursuit through large-scale genomic studies of carotid atherosclerosis as a distinct phenotype. Key Words: atherosclerosis Ⅲ genes Ⅲ human Ⅲ carotid artery Ⅲ cardiovascular disease I dentification of genes influencing complex clinically manifest traits such as myocardial infarction and stroke has been difficult, in part because of the many interacting factors known to contribute to these traits and the large conceptual, physiological, and temporal distance between gene variation and clinical manifestation of adult disease. 1,2 In addition, genetic analysis of a disease end point is complicated by vagaries in disease diagnosis, including variations in presentation, access to care, and acumen of care providers. Studies of phenotypes further upstream in the pathway from DNA sequence variation to overt clinical disease, such as ultrasonographic carotid atherosclerosis, may thus yield valuable information not obtainable by studying clinical conditions alone.Intimal-medial thickening (IMT) of the carotid artery determined by B-mode ultrasonography is a quantitative measure of atherosclerosis that has a graded, predictive relationship to overt clinical disease. 3 Carotid IMT can be measured noninvasively in population-based samples free of many of the biases of clinically identified cases and controls. [3][4][5] Focal carotid wall thickening (plaque) and lumen narrowing (stenosis) can also be imaged and also predict cardiovascular events. 6 Ultrasonographic measures of the carotid artery may thus provide a useful intermediate phenotype for the identification of atherosclerosis-related genes. In this review, we describe the most commonly reported ultrasound-defined carotid phenotypes and estimates of their heritabilit...