Hepatocellular carcinoma (HCC) and hepatoblastoma (HB) are malignancies of the liver with different etiologies, but the HB cell line HepG2 has been frequently used in various studies of HCC. In this study, we compare the protein expression patterns between HepG2 cells and three HCC cell lines, HKCI-2, HKCI-3, and HKCI-4, respectively. The cell lysates of individual cell lines were separated by two-dimensional polyacrylamide gel electrophoresis. The protein spots in the gel images were quantified and compared by image analysis software. The differentially expressing proteins were then identified by tryptic peptide mass fingerprinting. Compared with the HepG2 cells, the normalized quantities of 49 and 58 protein spots were found to be at least twofold higher and twofold lower, respectively, in all three HCC cell lines. The differentially expressed proteins can be grouped into structural proteins (annexins, transgelin, laminin receptor), stress-induced proteins (HSP27, 60, and 70), enzymes (aldehyde dehydrogenase, pyruvate kinase, α-enolase, etc.), and transcription factors (far upstream element binding protein 2, GTP-binding nuclear protein RAN). Some of these proteins play important roles in regulating homeostasis, drug resistance, apoptosis, cell differentiation, cell growth, and metastasis. In conclusion, our proteomic data indicate that there are considerable differences in the protein expression patterns between HepG2 cells and the HCC cells, suggesting differences m cellular properties. Hence, HepG2 may not be a good cell line model for studying HCC. Copyright © Humana Press Inc. All rights of any nature whatsoever are reserved.