Analysis of Hepatitis C Virus (HCV)-infected hepatocytes at the cellular level may contribute to elucidate the mechanisms of HCV pathogenesis. In this work, the presence of HCV components and pathological reactions in apoptotic hepatocytes from chronic HCV-infected patients were studied by electron microscopy and confocal microscopy. Eight samples of liver biopsies from patients with chronic hepatitis C were studied by laser scanning confocal microscopy, Transmission Electron Microscopy (TEM) and Immunoelectron Microscopy (IEM). Data provide evidence for apoptosis of hepatocytes from HCV-infected liver biopsies during chronic HCV infection. Confirmation of this process was based on the morphological data by TEM including cell shrinkage; chromatin condensation; formation of apoptotic bodies; phagocytosis by neighbouring cells; and the presence of DNA fragmentation by TUNEL assay and caspase 3 activation. Interestingly, Hepatitis C core protein (HCcAg) was specifically immunolabeled in the rough endoplasmic reticulum, mitochondria as well as in the nucleus of apoptotic hepatocytes. In addition, E1 was specifically immunostained in the cytoplasm and in the mitochondria of some hepatocytes. The presence of Crystalloid Bodies (CB) similar to those observed in recombinant P. pastoris expressing HCcAg was observed in the cytoplasm of some hepatocytes. Immunogold labelling showed that HCcAg co-localized with these CB. In addition, structures forming a paracristalline array and particles with a diameter of 50 nm appeared in the mitochondria of some apoptotic hepatocytes. Moreover, unstructured large aggregates containing HCcAg similar to those detected at late stages of HCcAg expression in recombinant P. pastoris cells were frequently observed in damaged hepatocytes. Of note, these aggregates were specifically immunostained with anti-HCcAg. Data suggest the possibility for a direct role of these HCV-related structures as well as HCcAg and E1 in apoptosis and pathogenicity.