The balance between a direct cytopathic effect by hepatitis C virus (HCV) and immune-mediated injury remains unclear. This report aims to test the following hypotheses: (1) that intrahepatic HCV load would correlate with the degree of liver injury; (2) that interferon alfa (IFN-alpha) would decrease intrahepatic HCV-RNA levels. Liver tissues (n = 56) were obtained from 47 patients with chronic HCV (9 before and after IFN-alpha therapy). Total RNA was isolated and quantitated for specific HCV RNA by dot-blot polymerase chain reaction (DB-PCR) using a standard curve created from synthetic HCV RNA of known titer to calculate actual RNA levels. A multivariate analysis was undertaken to determine the relationship of intrahepatic HCV-RNA levels with risk factors, length of HCV exposure, and histological injury scores. The confounding effect of HCV genotype was examined by direct sequencing of the NS5b region. Liver HCV RNA ranged from 10(2) to 3.1 x 10(7) molecules per microgram total liver RNA. The multiple regression analysis showed no effect of length of HCV exposure, risk factors, degree of bile duct damage, steatosis, or total Scheuer or Knodell score on RNA levels. No significant confounding effect of HCV genotype on the degree of liver injury was observed. However, genotype 1b had a significantly higher mean intrahepatic HCV-RNA load compared with the other genotypes detected. In the 9 patients who received IFN-alpha, treatment, 7 had no detectable HCV after treatment. This was associated with a significant decrease in intrahepatic HCV-RNA levels (7.57 +/- 2.53 X 10(5) to 1.82 +/- 1.80 x 10(3) molecules per microgram total liver RNA +/- SEM, n = 9, P = .0005). These results do not directly support our hypothesis that increased intrahepatic HCV load is associated with more severe liver injury. Intrahepatic viral load appears to be significantly increased in patients with genotype lb. IFN-alpha treatment does significantly lower intrahepatic HCV load.