Infection with putative non-A to E hepatitis virus, designated GB virus C (GBV-C), was surveyed in 286 patients with chronic liver disease in Japan. RNA of GBV-C was detected, by reverse-transcription polymerase chain reaction with nested primers from the 5'-noncoding region, in 19 patients (6.6%) at a frequency higher (P < 0.001) than in three of 275 (1.1%) normal controls. It was detected in three of 83 (4%) patients with hepatitis B virus infection, 15 of 188 (8%) patients with hepatitis C virus infection, and one of 12 (8%) patients without evidence of ongoing infection with hepatitis B or C virus. GBV-C RNA was detected in nine of 186 (5%) patients with chronic hepatitis aged 51.2 +/- 13.3 years, six of 64 (9%) with liver cirrhosis aged 62.9 +/- 11.4 years, and four of 36 (11%) with hepatocellular carcinoma aged 62.0 +/- 11.1 years. Nucleotide sequences of 100 base pairs in the helicase region of GBV-C isolates from the 19 patients varied up to 21%, while sequences of 33 deduced amino acids were conserved and differed only by up to 6%. These results indicate that infection with GBV-C in patients with non-B, non-C chronic liver disease would not be frequent, although the sensitivity of the detection method could be improved. Coinfection of GBV-C with hepatitis B or C virus, as well as the duration of infection, might accelerate the progression of chronic liver disease.