Aim: The present study examined the differential expression of proteins in HuH-7 cells and HUH-7 cells harboring in vitro-transcribed full-length hepatitis C virus 1b RNA (HuH-7-HCV), and elucidated the cellular responses to HCV replication. Methods: The protein profiles of matched pairs of HuH-7-HCV cells and HUH-7 mock cells were analyzed by 2-D electrophoresis (2DE). Solubilized proteins were separated in the first dimension by isoelectric focusing, and by 12.5% SDS-PAGE in the second dimension. The differential protein expression was analyzed by use of image analysis software to identify candidates for HCV infection-associated proteins. Results: In total, 29 protein spots showed increases and 25 protein spots showed decreases in signal in HuH-7-HCV cell 2DE profiles as compared with HuH-7 mock cells. In the next step, the 10 spots showing the greatest in-crease and the 10 spots showing the greatest decrease were excised from gels and the proteins present were identified by Matrix-Assisted Laser Desorption/Ioniza-tion Time of Flight Mass Spectrometer (MALDI-TOF MS) or MALDI-TOF/TOF MS. In total, 13 proteins were identified successfully. The potential significance of the differential expression due to HCV replication was discussed. Conclusion: Our study identifies changes in the proteome of HuH-7 cells in the presence of HCV replication and yields information of the mechanism of HCV pathogenesis. These results will be useful for the identification of HCV infection-associated proteins that could be molecular targets for treatment.