In order to investigate the distribution of Hepatitis C virus (HCV) genotypes in Thailand, we performed phylogenetic analysis based on the virus core region and in this way we identified and reliably distinguished HCV genotypes 1-6 as well as subtypes. Among 100 plasma samples randomly selected from blood donors positive for antibodies to HCV (anti-HCV) 90 (90%) were found positive for HCV RNA and 77 of them were subjected to nucleotide sequencing. The following types and subtypes were identified in this group: 1a in 16 samples (20.8%), 1b in 14 samples (18.2%), 3a in 29 samples (37.7%), 3b in 5 samples (6.5%), and 6a in 13 samples (16.9%). Although this study allowed identification and characterization of HCV among blood donors, more extensive studies are needed to explore the HCV distribution in other population groups and in other geographical regions and to exploit the virus core-based characterization of HCV for evaluation of treatment and clinical outcome and epidemiological purposes.