That genetic factors contribute to the onset and progression of chronic diabetic complications is highly convincing, but the gene or genes conferring susceptibility to these diseases remain to be identified. To identify genetic elements that might confer susceptibility to diabetic nephropathy, we performed a genome-wide analysis of gene-based single nucleotide polymorphisms (SNPs) in a large cohort of Japanese diabetic patients. In case-control association studies, patients with type 2 diabetes were divided into two groups, one having retinopathy as well as overt nephropathy and the other (the control group) with diabetic retinopathy but with no signs of renal involvement. Genotyping of these patients at more than 80,000 SNP loci suggested several distinct regions to be good candidates for the susceptibility to diabetic nephropathy. The results indicated that genome-wide search using SNP as a genetic marker is useful to identify the gene(s) susceptible to common diseases such as diabetic nephropathy.