The genome-based study of human disease has been developing rapidly with the completion of the human genome project and the remarkable progress of technology. The genetic variation information associated with disease will certainly enable us to discover potential drug targets and to develop personalized medicine. Chronic kidney disease (CKD) is now recognized as a public health problem because its prevalence is increasing all over the world. No treatment can reverse the progression of CKD to end-stage renal disease (ESRD), which requires enormous medical resources. Moreover, CKD is known to be a strong risk factor for cardiovascular disease. In this review, we summarize the genetic studies that have reported a number of disease susceptibility genes and loci for CKD and ESRD. Earlier investigations, mostly by linkage analysis and association analysis with candidate gene approaches, have demonstrated that genetic factors play a crucial role in CKD and ESRD. However, the findings have contributed little great impacts related to drug discovery and diagnostic tool development in kidney diseases: further investigations are necessary to confirm the previously identified susceptibility genes. Recent technological advances will enable us to perform genome-wide association analysis, discover new disease susceptibility genes, and establish novel treatment strategies based on genomic information related to kidney disease.