Several epitopes of the hepatitis C virus (HCV) have been identified, but the biological and clinical significance of antibodies to each protein is not well understood. Core antigens include C-22, JCC, P 0 and CP-9. Among epitopes in the non structural (NS) regions, C-33C is in the NS3, C100-3 in the NS3/4, 511 in the NS4 and C825 in the NS5 regions. First generation anti-HCV has C100-3 epitope and second generation anti-HCV consists of three epitopes which are C-22, C-33C and C100-3. In order to analyse the clinical significance of the various HCV epitopes, We compared the results of these 9 different HCV specific assays with HCV-RNA, as determined in serum by RT-PCR method using primers to the 5' untranslated region of HCV-RNA. Among 73 patients with chronic NANB liver disease, 94% were positive for C-22, 94% for JCC, 91% for P 0, 89% for CP-9, 97% for C-33C, 84% for C100-3, 65% for 511, 55% for C825, 58% for GOR and 91% for RT-PCR. Positive rates for Core region epitopes were very similar to each other and to the presence of HCV-RNA. Antibodies to NS region epitopes were more variable, with those to NS4 and NS5 region being less sensitive than HCV-RNA. Positivity rates for 537 healthy subjects were 1.1% for C100-3, 2.7% for JCC. 6 persons who were positive for C100-3 were also positive for JCC and 4 of those were positive for HCV-RNA.(ABSTRACT TRUNCATED AT 250 WORDS)