Antibody to the hypervariable region (HVR) of HCV is thought to have neutralizing activity. The HCV genotype is known to affect the clinical course of infection. The antibody response to HVR and its relationship to the virologic and clinical characteristics were investigated in 21 patients with chronic hepatitis C. HVRs amplified by polymerase chain reaction from serum HCV were expressed as glutathione S-transferase fusion proteins. From 8 to 34 clones per serum sample were obtained (375 clones total), and the anti-HVR antibody in serum was assessed by Western blot. Both the incidence of fusion proteins positive for anti-HVR antibody and the activity of antibody were significantly higher in 6 patients with genotype 2a than in 15 patients with genotype lb. This result suggests that the quantity of humoral response to HVR affects the clinical outcome of infection with these two HCV genotypes.