We analyzed hepatitis C virus (HCV) obtained from a healthy HCV carrier in an aboriginal community with high prevalence of HCV infection. By use of random primers and specific oligonucleotide primers, a cDNA fragment of putative non-structural 3 (NS3) region of the HCV genome was cloned by reverse transcription-polymerase chain reaction (RT-PCR) using RNA extracted from a serum sample of a healthy HCV carrier in Taur-Yuan village. The nucleotide and deduced amino acid sequences from the 583 nucleotides long cDNA were compared with those of equivalent region of HCV of other previously reported clones: [J1, HCV-J (regarded as major type of HCV in Japan) and US prototype]. They had 93.7% (546/583), 93.1% (543/583) and 80.4% (469/583) homology at the nucleotide level and 96.9% (188/194), 96.9% (188/194) and 91.8% (178/194) homology at the amino acid level, respectively. These results showed that HCV prevalent in an aboriginal community in Taiwan is more similar to Japanese type than to the US prototype.