Objective: Hepatocellular carcinoma (HCC) is the seventh most common cause of cancer and the third fatal cancer worldwide. Hepatitis B virus (HBV) and hepatitis C virus (HCV) are the most common cause of HCC. Although HBV and HCV can be cause HCC in long time but they are different viruses and use different mechanisms for liver carcinogenesis. The aim of this study was to identify proteins that are differentially expressed in sera from HCC patients related to HBV and HCV by two dimensional polyacrylamid gel electrophoresis (2D- PAGE) and liquid chromatography tandem mass spectrometry (LC-MS/MS). Materials and Methods: Twelve Sera from HCC patients related to HBV and HCV were subjected to 2-DE- PAGE. After silver staining, gels were scanned with GS-800 scanner and analyzed by Progenesis software for finding differentially expressed proteins. Differentially expressed proteins picked up from gels, destaiend and were identified by LC-MS/MS instrument and spectrum Mill software. Results: We found that HCC patients related to HBV and HCV had different serum protein patterns. Seventh spots were differentially expressed between two groups more than 1.5 fold, that 12 of them identified by LC-MS/MS including 3 isomeres of luecine rich-α2 glycoprotein, 2 isomer of haptoglobin alpha and transthyretin. Conlcussion: Our data showed that sera from HCC patients related to HBV and HCV have different protein patterns. These differentially expressed proteins maybe related to different mechanisms which involve in hepatocarcinogeneses and could be useful as diagnostic and/or prognostic biomarker for HCC with different viral origin.