In this study, we showed that the most dominant subcellular location for HCV core, NS5A, and NS5B proteins was in the mitochondria, followed by the ER and the Golgi. Consequently, expression of HCV core or non-structural proteins led to increased ROS generation in the mitochondria, which most likely contributed to mitochondrial injury and degeneration. Expression of non-structural proteins also led to membrane blebbing in the ER and accumulation of autophagocytic vacuoles. Despite these changes, only cells with the subgenomic replicon (i.e. cells expressing the non-structural proteins) showed consistent upregulation of mitochondrial and cytosolic antioxidant enzymes. Cells with the genome-length replicon, on the other hand, did not have a robust antioxidant response and showed prolonged population doubling time and a decrease in cyclin D1 expression. Apart from the shared mitochondrial phenotype, increased lipid accumulation was also common among all three HCV proteinexpressing cell lines. Subcellular locations of HCV proteins have provided important clues to the site of viral genome replication and assembly, as well as the cytopathic effects caused by HCV infection. The ultrastructure study with immunogold labeling showed a distinct localization of core, NS5A, and NS5B proteins in the mitochondria and the ER. Significant core, NS5A, and NS5B distributions were observed in other subcellular compartments, including the Golgi apparatus, the nucleus, and lipid droplets. The study results are in general agreement with previously published data [26] [27] [28] [29] [30] [31] . However, the inner membrane location of core protein was unexpected because previous studies using proteinase K digestion suggested association of core protein with the mitochondrial outer membrane and the mitochondrial-associated membrane compartment [15, 28] . The discrepancy could be due to the compromised mitochondrial membrane integrity in genome-length replicon and Core-on cells, or due to artifacts from sample preparations for EM analysis. The association of core protein with lipid droplets also appeared to be lower than previous study results, and the discrepancy could be due to differences in the antibodies used.