Coronary artery disease is a common condition with a known heritable component that has spurred interest in genetic research for decades, resulting in a handful of candidate genes and an appreciation for the complexity of its genetic contributions. Recent advances in sequencing technologies have resulted in large-scale association studies, possibly adding to our current understanding of the genetics of coronary artery disease. Sifting through the statistical noise, however, requires the selection of effective phenotypic markers. New imaging technologies have improved our ability to detect subclinical atherosclerosis in a safe and reproducible manner in large numbers of patients. In this article, we propose that advances in imaging technology have generated improved phenotypic markers for genetic association studies of coronary artery disease.