This study aims to clarify the prevalence and significance of the emergence of hepatitis B virus (HBV) pre-S/S mutations in children with hepatitis B virus-associated membranous nephropathy (HBVMN). Direct sequencing of polymerase chain reaction products of renal tissue samples that were obtained via percutaneous renal biopsy from seven children revealed the presence of HBV DNA. Seven adr subtypes were analyzed. Deletions in the HBV pre-S region were observed once per seven patients. The deletions were noted in both the pre-S1 (27 bp) and pre-S2 (60 bp) regions. Various point mutations in the HBV pre-S region were detected in all seven patients and proved to be more frequent in the pre-S1 region than in the S2 region. Point mutations in the HBV S region were detected in six patients. Among these mutations, the mutation in the “a” determinant region was noted in five patients. No deletion, however, was observed in the HBV S region. These observations suggested that deletions and point mutations in the HBV pre-S1 and pre-S2 regions and point mutations in the HBV S region, especially the “a” determinant region, are common frequent findings. These results also suggested that HBV pre-S/S region mutations may be involved in the pathogenesis in children with HBVMN.