Hepatitis B virus (HBV)-associated nephropathy is considered as an immune-mediated disorder which is dependent on interactions between viral, host, and environmental factors. But there are few reports that investigated the relationship between the development of HBV-associated nephropathy and HBV genotypes and the mutations. To clarify the relationship between nephropathy and HBV genotype in Japan, six male patients with HBV-associated nephropathy were examined. The complete genome sequences of HBV were determined directly and the specific mutations associated with the development of HBV-associated nephropathy were examined by comparison of the alignments along with consensus sequences [HBV/A1 (Aa), A2 (Ae), B1 (Bj), B2 (Ba), C1 (Cs) and C2 (Ce)] retrieved from international database. The mean age of the six patients was 33.5 years. HBeAg was found in all patients and serum HBV-DNA levels were relatively high. Histological findings of renal tissues indicated five cases of membranous nephropathy and one membranoproliferative glomerulonephritis. HBV genotypes from the six patients were two HBV/A1, two A2 and two C2, suggesting HBV/A was predominant. G1862T mutation was observed in the two HBV/A1 patients, resulting in the pre-core amino acid substitution with a switch from valine (Val) to phenylalanine (Phe). Only one patient had core deletions. It is concluded that HBV/A may be associated with membranous nephropathy, but little relationship between HBV gene mutations and the development of HBV-associated nephropathy was observed.