The so-called interferon sensitivity determining region (ISDR) in the NS5A protein of hepatitis C virus (HCV) undergoes mutational changes in chronically infected hosts, but its mechanism remains obscure. We analyzed the ISDR by direct sequencing and/or restriction fragment length polymorphism in serial sera from two patients with chronic hepatitis C. Patient 1 showed a change in the ISDR quasispecies from wild type to mutant type, while in patient 2 the situation was vice-versa, during a period where interferon was not administered. The emerging mutant in patient 1 was detected in IgG-unbound HCV fraction, while the fading-out mutant in patient 2 was IgG-bound. These results suggest that an immune pressure against virion surface epitope(s) plays an insidious role for the apparent selection of HCV ISDR quasispecies. Of note, the ISDR mutants found in the two patients, irrespective of IgG-bound or -unbound, disappeared promptly by interferon therapy.