The nature and distribution of hepatitis C virus (HCV) genotypic variants present in south-east Asia have not been extensively investigated. We analysed HCV RNA obtained from 67 clinical serum samples from Singapore, Thailand, Indonesia, the Philippines and South Korea. All samples were amplified by semi-nested RT-PCR and the nucleotide sequence determined for four regions within the E1, E2/NS1, NS4 and NS5 genes. Each isolate had a unique nucleotide and deduced amino acid sequence, consistent with the genetic heterogeneity of this virus. There was remarkably little amino acid sequence variation between isolates of the same genotype, apart from variable domains within putative envelope glycoproteins that are likely to be under immune pressure. All isolates could be classified according to the currently recognized genotypes of HCV, with the exception of one Singapore isolate that defined a new group 3 subtype. The 1b genotype, which predominates in Japan, was the most widely distributed genotype and accounted for 58% of all isolates sequenced. Regional variations in HCV genotype distribution were observed, with type 3a being found almost exclusively in Thailand. By contrast, the 1a genotype, which predominates in the USA was the most prevalent genotype in the Philippines. Genotype 1a was found less commonly among the Thai isolates, presumably having been introduced from the West in stored blood products or by sporadic transmission. The significant prevalence of HCV types 2 and 3 restates the need for variant genotypes to be included in immunodiagnostic and vaccine development strategies. This study reveals that the 1b genotype of HCV, previously found to be the major variant present in east Asia, also predominantes in the south-east Asian region, and may be the major HCV type found worldwide.