We studied the prevalence of GB virus C/hepatitis G virus (GBV-C/HGV) infection among 112 patients with liver disease and 121 blood donors in Ulaanbaatar, Mongolia. Reverse transcription and polymerase chain reaction were employed to detect GBV-C/HGV RNA using the specific primers derived from the 5'-untranslated region (5'-UTR) of the GBV-C/HGV genome. Nucleotide sequences of all positive samples for GBV-C/HGV RNA were determined. The sequences were analyzed by a molecular evolutionary method. Twenty-five (10.7%) of 233 people were positive for GBV-C/HGV RNA. Eight (6.6%), 11 (9.1%), and 30 (24.8%) blood donors were positive for GBV-C/HGV RNA, HBsAg, and anti-HCV, respectively, although 17 (15.2%), 65 (58.0%), and 64 (54.5%) patients with liver disease were positive for each viral marker. The prevalences of GBV-C/HGV RNA, HBV, and HCV in the patients were significantly higher than those in blood donors (P < 0.05). There was no significant difference in the prevalence of anti-HCV among people with and without GBV-C/HGV RNA, while the prevalence of HBsAg among people with GBV-C/HGV RNA was significantly higher than among those without GBV-C/HGV RNA (P < 0.05). The molecular evolutionary tree showed that GBV-C/HGV was a heterogeneous virus and all strains could be divided into 2 types. One is the same phylogenetic type as HGV, and the other is a new type that is different from GBV-C and HGV.