Background Polymorphisms of GJA4 and CYBA and of PAI1 and MMP3 are associated with myocardial infarction (MI) in men and women, respectively. In addition, several polymorphisms associated with restenosis after percutaneous coronary intervention, coronary artery spasm, or hypertension have been identified. More recently, a large genetic epidemiological study was performed to identify additional gene polymorphisms that confer susceptibility to cardiovascular diseases, stroke, and other complex diseases. Methods and Results The relationship of 202 polymorphisms in 152 candidate genes to MI, hypertension, ischemic or hemorrhagic stroke, metabolic syndrome, type 2 diabetes mellitus, obesity, or in-stent restenosis were examined in 5,000 unrelated Japanese individuals. Of these, 14 polymorphisms related to MI, 8 to atherothrombotic cerebral infarction, 9 to intracerebral hemorrhage, and 10 to subarachnoid hemorrhage were identified. This information was then used to develop risk diagnosis systems to predict the future risk for development of each disease in a given individual. Conclusions Identification of gene polymorphisms that confer susceptibility to cardiovascular diseases or stroke and the development of genetic risk diagnosis systems may contribute to the personalized prevention of these conditions.