The heart diseases that account for a large amount of morbidity and mortality in the developed world (coronary artery disease, myocardial infarction and heart failure) are phenotypically heterogeneous disorders. It has been suspected for many years that genetics may have an important role in these diseases and their poor outcome. However, their complex and likely polygenic pathophysiology has confounded clear understanding of the genetic contribution to their etiology. Despite technological progress and great promise associated with genome-wide association studies, to date the results of their application to coronary artery disease, myocardial infarction and heart failure have yielded limited insights into these common diseases. This review discusses the current status of genome-wide association studies as they have been applied to these cohorts. The potential limitations of these studies, as well as potential future directions for identifying important genes are also discussed.