The incidence of hepatocellular carcinoma (HCC) is highest among primary liver cancer. HBV and HBV-induced liver cirrhosis may lead to HCC[1]. At present, it is difficult to diagnose HCC at early stage or to differentiate HCC. Therefore it is urgent to explore and develop a simple, rapid diagnostic method, which has higher sensitivity and specificity for HCC at early stage([2]). Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF-MS) is a novel non-electrophoresis-based proteomic technology. SELDI offers the advantages of rapid and simple examination as well as high specificity and sensitivity([3]). To our knowledge,there has been little study reported using SELDI-TOF-MS technology to investigate HCC. In this study, 25 cases of the patients with HCC without receiving any therapy, 25 cases of the patients with HCC receiving the interpose chemotherapy and 50 cases of the healthy people were tested by Weak cationic exchange (WCX2) protein chip and SELDI-TOF-MS. The differentially expressed proteins were analyzed by BioMarker Wizard. At the different M/Z value range, seven proteins were obviously different in the group of the patients with HCC without receiving any therapy, the patients with HCC receiving the interpose chemotherapy and the healthy people. Analyzing by BioMarker Wizard software, four proteins including 6 489.48 Da, 6 662.34 Da, 8 593.75 Da and 8 720.23 Da were up-regulated in healthy controls, two including 7 777.27 Da and 9 250.00 Da were up-regulated in the patients with HCC without receiving any therapy and one 16 200.17 Da was up-regulated in the patients with HCC receiving the interpose chemotherapy. By use of Bio-marker Pattern, two protein profiles (7 777.27 Da, 9 250.00Da) that can separate patients with HCC without receiving any therapy from normal controls have been developed. They gave the much-improved sensitivity of 92% and the specificity of 100%. Through searching database, these seven proteins were identified to might be Galanin related peptide, Pro-neuregulin-4 protein, small inducible cytokine A15 precursor, 9 kDa protein, CSL-zincfinger protein 1, mitochondrial hinge protein, actin related protein, respectively. Using SELDI-TOF-MS, the method of sieving the tumor markers from HCC becomes quick and valid. These differential proteins could be biomarkers of HCC in the serum and drug targets for treating HCC.