The recently discovered GB virus C/hepatitis G virus (GBV-C/HGV) has been shown to be scarcely associated with hepatitis, though its possible pathogenesis remains unknown. In previous report, we designed primers for semi-nested reverse transcription-polymerase chain reaction (RT-PCR) to detect 5'-noncoding region of GBV-C/HGV, and screened the sera from 45 patients with liver diseases or on hemodialysis. In this study, we studied the prevalence of GBV-C/HGV infection in the sera from 35 patients with hemophilia A by this RT-PCR method, and also performed sequence analysis for all isolates including those from the non-hemophilic patients previously reported. GBV-C/HGV was detected in 8.57% (3/35) of the hemophilic patients. The isolates from hemophilic patients had several common mutations, and these mutations were also common in the "West African" genotype isolates represented by the prototype GBV-C. However, sequences in the isolates from other positive patients with liver diseases or on hemodialysis were quite different from those in the isolates from hemophilic patients, and those in the "European/American" genotype isolates represented by the prototype HGV. These sequences were consistent with "Asian" genotype. Simple restriction fragment length polymorphism (RFLP) analysis using the restriction enzyme HhaI successfully discriminated these genotypes. In the hemophilic patients, GBV-C/HGV might have been transmitted by transfusions of the imported plasma-derived clotting factor concentrates. Thus the difference in GBV-C/HGV genotype between the hemophilic patients and the others is suggested to be related to transmission route.