RNA of a putative non-A, -B, -C, -D, or -E hepatitis virus named GB virus C (GBV-C) was detected by reverse transcription-polymerase chain reaction with primers deduced from the 5' untranslated region in 15 (24%) of 63 men with hemophilia in Japan at a frequency higher (P < .001) than that in 2 (0.6%) of 337 controls. By phylogenetic analysis, GBV-C isolates from some patients were similar in sequence, indicating infection with closely related strains, and those from certain patients resembled sequences reported from foreign countries. All patients were infected with hepatitis C virus, and genotypes that are rare in Japan were detected in 36 (57%) of them. These results indicate that patients with hemophilia in Japan would be at increased risk for infection with GBV-C and hepatitis C virus, some of which would have been transmitted via imported coagulation factor concentrates in the past.