The role of virus-related apoptosis in hepatic injury in chronic HCV is unclear. It is unknown whether HCV induces apoptosis directly or whether cellular injury is immunologically mediated. We studied the relationship between infected hepatocytes, apoptosis and necroinflammation. We established a Fluorescence Activated Cell Sorter (FACS) based intracellular staining technique for the HCV NS3 protein and examined intrahepatic viraemia, disease activity and apoptosis. We also stained infected cells for expression of human leucocyte antigen (HLA) class I and Fas antigens. We examined 34 liver biopsies (24 from patients with HCV) and found marked variation in the proportion of infected cells (2.5-42%). The number of infected cells correlated with serum viraemia but not histology. The number of infected cells was inversely related to the number of apoptotic cells (P < 0.001); infected cells expressed both HLA class I (14 cases) and Fas antigens (12 cases). The number of hepatocytes infected with hepatitis C is variable and does not influence histological activity. In infected patients, the majority of HCV-positive hepatocytes express target molecules for activated lymphocytes (Fas and HLA class I antigens) but they do not undergo apoptosis, suggesting that hepatitis C may inhibit apoptosis by modulating intracellular pro-apoptotic signals.