AIM: To find out potential serum hepatocellular carcinoma (HCC)-associated proteins with low molecular weight and low abundance by SELDI-based serum protein spectra analysis, that will have much application in the diagnosis or differentiated diagnosis of HCC, as well as giving a better undersyanding of the mechanism of hepato-carcinogenesis. METHODS: Total serum samples were collected with informed consent from 81 HCC patients with HBV (+)/cirrhosis(+),36 cirrhosis patients and 43 chronic hepatitis B patients. Serum protein fingerprint profiles were first generated by selected WCX2 protein chip capture integrating with SELDI-TOF-MS, then normalized and aligned by Ciphergen SELDI Software 3.1.1 with Biomarker Wizard.. Comparative analysis of the intensity of corresponding protein fingerprint peaks in normalized protein spectra, some protein peaks with significant difference between H.CC and cirrhosis or chronic hepatitis B were found. RESULTS: One hundred and twenty-eight serum protein peaks between.2000 and 30000Da were identified under the condition of signal-to-noise＞5 and minimum threshold for cluster＞20%.Eight-seven of these proteins were showed significant differences in intensity between HCC and cirrhosis (P＜0.05＝.Of the above differential proteins, 45 proteins had changes greater than two-fold, including 15 upregulated proteins and 30downregulated proteins in HCC serum. Between HCC and chronic hepatitis B,9 of 52 differential proteins (P＜0.05＝ had intensities of more than two-fold, including 2 upregulated proteins and 7 downregulated proteins in HCC serum. Between cirrhosis and chronic hepatitis B,28 of 79 significant differential proteins (P＜0.05＝ changes greater than two-fold in intensity, including 17 upregulated proteins and 11 downregulated proteins in cirrhosis serum. For the analysis of these leading differential proteins in subtraction difference mode among three diseases, the five common downregulated proteins in HCC serum (M/Z 2870,3941,2688,3165,5483) and two common upregulated proteins (M/Z 3588,2017) in HCC and cirrhosis serum were screened. CONCLUSION: Because the interference of unspecific secreted proteins from hepatitis B and cirrhosis could be eliminated partly in HCC serum under subtraction difference analysis, these seven common differential proteins have the obvious advantage of specificity for evaluating the pathological state of HCC and might become novel candidate biomarkers in the diagnosis of HCC.