To investigate the relationship between genotypes of hepatitis C virus and response to interferon-a therapy, hepatitis C virus RNA was assayed by polymerase chain reaction with three sets of primers and probes in 70 patients with non-A, non-B chronic hepatitis who received interferon-a. Twenty-four patients sustained long-term remissions (complete responders). Polymerase chain reaction for 5'-terminal noncoding region detected hepatitis C virus RNA in 94.3% (66 of 70) of the patients. Polymerase chain reaction for nonstructural region 3, in which primers and a probe were synthesized to be identical to hepatitis C virus-J, detected hepatitis C virus RNA in 40 patients. Polymerase chain reaction for nonstructural region 5-in which sequences of primers and a probe were derived from hepatitis C virus-K2, a genotype different from hepatitis C virus4detected hepatitis C virus RNA in 17 patients. Only one patient was positive on both nonstructural region 3 and nonstructural region 5 polymerase chain reaction. Nucleotide sequence of clones obtained from 5' terminal noncoding region polymerase chain reaction products of two patients positive on polymerase chain reaction for nonstructural region 3 and negative on polymerase chain reaction for nonstructural region 5 (group 1) corresponded to that of the hepatitis C virus-J group, and those of clones from two patients negative on polymerase chain reaction for nonstructural region 3 and positive on polymerase chain reaction for nonstructurd region 5 (group 2) corresponded to that of hepatitis C virus-K!Z. A clone from a patient negative on polymerase chain reaction for nonstructural region 3 and polymerase chain reaction for nonstructural region 6 ( w u p 3) showed low nucleotide sequence homology with the hepatitis C virus4 and hepatitis C virus-K2 groups. The complete response rates of group 2 (10 of 16 [62.5%]) and group 3 (6 of 10 [60.0%1) were signiscantly higher than that of group 1 (5 of 39 [ 12.8%]) (p < 0.01 for both). Logarithms of hepatitis C virus RNA concentrations (copies per milliliter) were