We investigated the fluctuation of hepatitis C virus (HCV) quasispecies during interferon therapy by single strand conformation polymorphism (SSCP) analysis. In 13 of 16 interferon ineffective patients, the predominant HCV population was replaced with other quasispecies during the treatment. Especially, in 9 patients, a part of the HCV quasispecies, pre-existing before interferon therapy, became predominant after the therapy. These results indicate that sensitivity to interferon differs among HCV quasispecies and that interferon selects resistant HCV strains. Existence of such HCV quasispecies seems to be associated with interferon treatment failure.