The prevalence of TT virus (TTV) and GB virus-C/hepatitis G virus (GBV-C/HGV) infection and the association with raised liver function tests in 546 Taiwanese with negative HBsAg, anti-HCV and HCV RNA was elucidated. They were tested for serum alanine aminotransferase (ALT), GBV-C/HGV RNA, anti-envelope protein 2 antibody (anti-E2) and TTV DNA. Direct sequencing and phylogenetic analyses were performed on 58 isolates for TTV genotype determination. The prevalence of TTV DNA, GBV-C/HGV RNA, anti-E2 and over all GBV-C/HGV exposure was 24.9, 3.4, 8.2 and 11.1%, respectively. Using uni- and multi-variate analyses, male gender and TTV viremia were associated significantly with raised ALT values. Sixty-nine percent of TTV isolates were deduced to be TTV genotype 1 and they had significantly lower mean age than genotype non-1 isolates. In the population, raised ALT may be related to male gender and be attributable to TTV infection but not to GBV-C/HGV among individuals with no evidence of current HBV and HCV infection. TTV genotype 1 is the most prevalent genotype and associated with younger age.