Recent research suggests that many genetic variants and environmental exposures can influence the occurrence and progression of common diseases, including stroke. However, the genetic risk factors for ischemic stroke, the most common type of stroke in developed countries, are almost unknown. We conducted a genome-wide association study using 1112 Japanese subjects who has suffered from ischemic stroke. Age- and sex-matched healthy individuals were selected as controls from the participants of the health examination survey conducted in the Hisayama study in 2002-03. We used a two-stage screening method and identified 2 genes related to the susceptibility of ischemic stroke: PRKCH and AGTRL1. A non-synonymous single nucleotide polymorphism (SNP) in the PRKCH gene (rs2230500, V374I) was significantly associated with lacunar infarction in 2 independent case control samples. The nonsynonymous SNP altered the kinase activity of protein kinase C-eta (PKCeta). We also found that PKCeta; was mainly expressed in vascular endothelial cells and foamy macrophages in human atherosclerotic lesions and that its expression was enhanced as the lesion progressed. Four SNPs around the AGTRL1 gene were closely associated with ischemic stroke. An SNP in the promoter region (rs9943582) enhanced the expression level of AGTRL1 mRNA. A population-based cohort study with 14 years of follow-up revealed that functional SNPs of these genes were found to significantly increase the incidence of ischemic stroke. Therefore we suggest that genome-wide association study is a powerful tool for identifying new susceptibility genes and can provide new insights into the pathogenesis, prevention, and treatment of ischemic stroke.