The aim of this work was to study the prevalence, potential risk factors, clinical and laboratory features of GB virus C (GBV-C) infection in general population from an area endemic for hepatitis C. A reverse transcriptase-polymerase chain reaction (RT-PCR) for detection of GBV-C RNA was used to examine the prevalence of GBV-C RNA in both hepatitis C virus (HCV) endemic (R town) and nonendemic areas (M town) in Yamagata prefecture, Japan. In R town, GBV-C RNA was detected in 23 (2.9%) out of the 800 residents, whereas anti-HCV and HCV-RNA were found in 226 (28.3%) and 163 (20.4%), respectively. The prevalence of GBV-C RNA in R town (2.9%) was higher than that in M town (1.0%), although the difference was not statistically significant. The individuals with anti-HCV had significantly higher frequency of active GBV-C-infection than those without anti-HCV in both towns. No evidence indicating that GBV-C infection affected the severity of hepatitis C was obtained. The multivariate analysis revealed that the young anti-HCV positive individuals with a history of blood transfusion had higher incidence of active GBV-C infection. The phylogenetic analysis showed that the GBV-C isolates from both R and M towns were divided into two separate branch groups designated HG and Asia GB groups.