Hepatitis C virus (HCV) RNA was amplified and detected in the serum of 17 anti-HCV antibody positive patients using a single-stage (30 cycles) polymerase chain reaction (PCR). Specific amplification, targeted to the C-100 protein (anti-HCV) region, was confirmed by direct sequencing of the PCR product. Single-stage PCR detected the virus in 11 patients. Polymerase chain reaction-positive patients demonstrated a significantly higher histologic activity index (10.3 + 1.2 standard error of mean |SEM| than those testing negative (5.8 + 1.5 SEM, P < .05). Nine of 11 PCR-positive patients exhibited a rise in alanine transaminase (ALT) values within 1 month of assay, compared with only 1 of 6 PCR-negativc patients. The correlation between rising ALT levels and PCR positivity was significant (P < .01). Direct sequencing revealed mutability in all cases, some of which resulted in amino acid substitutions. The authors concluded that HCV detection using single-stage PCR correlates with biochemical and histologic features of disease activity. Mutability is likely an important feature of HCV pathobiology and may significantly affect detection methods.