Objective To understand the clinical significance of sequence variations in the hypervariable region (HVR) of hepatitis C virus during infection. Methods Eight patients with acute hepatitis C and 20 patients with chronic hepatitis C were followed up for two years. Blood samples were taken at intervals of six months for analysis of HCV-HVR sequences by reverse transcription-pelymerase chain reaction (RT-PCR) and direct sequencing methods. Results HCV-HVR sequences of the 28 patients changed in various degrees. 92% of these nuclentide substitutions led to changes of corresponding amino acid sequence. Only 8% of changed nucleotide were synonymous substitutions. Of 27 amino acids variation of amino acid ranged from 1 to 20 (mean 8, 30%). The most common nucleotide substitution (62%) occurred in the first position of codon, 31% in the second and the rest in the third. HVR variation rate wes 0.89×10-1 per genome site per year in acute hepatitis C, compared with 2.31×10-1 per genome site per year in chronic hepatitis C (P＜0.05), but had no relafian to HCV subtype. Variation of HVR in the flare up type (ALT＞150 μ/L) was much more than that in the quiescent type (ALT＜100 μ/L). Conclusion Our results suggested that sequence variation of HVR during HCV chronic infection seems to be an adaptive response to HCV to evade the host immune pressure and might play a major role in the establishment of persistent infection as well as in the flare-up of hepatitis.