A novel DNA virus, TT-virus (TTV), was isolated from a post-transfusion hepatitis patient in Japan. The prevalence of TTV infection was investigated among patients with chronic liver disease and normal alanine aminotransferase (ALT) volunteers as controls in Mongolia. Polymerase chain reaction (PCR) was employed to detect TTV DNA using specific primers derived from open reading frame 1 (ORF1) of the TTV genome. Nucleotide sequences of samples positive for TTV DNA were determined. The sequences were analyzed by a molecular evolutionary method. Fifty (60.2%) hepatitis patients and 12 (42.9%) volunteers were positive for TTV DNA. The serum ALT levels did not differ significantly between patients with single TTV infection and without TTV, HBV and HCV infection. Similarly, the serum ALT levels did not differ significantly between controls with and without TTV infection. Dual infection of TTV with either HBV or HCV did not affect the ALT levels of hepatitis patients. The molecular evolutionary tree showed that TTV was a heterogeneous virus and all strains could be divided into three genotypes in Mongolia. A new genotype was identified that was distinct from those previously reported.