Abstract: Objective To compare gene expression profiles among hepatocellular carcinomas(HCC), cirrhotic liver tissue and normal liver and analyze their biological information. Methods Total RNA was isolated from hepatocellular carcinomas, cirrhotic liver tissue and normal liver respectively, purified into mRNA by oligotex, and reverse-transcribed to synthetize two kinds of fluorescences (Cy3-dUTP, Cy5-dUTP) labeled cDNA probes. The targets were mixed together and hybridized with the genes on the genechip contained 4096 genes. The following comparisons were performed: hepatocellular carcinomas versus normal liver, cirrhotic liver versus normal liver. Genes that were differentially expressed between these groups were identified based on signal-to-noise ratios by using GenePix Pro3.0 software. Results 141 genes were found have closely relation to HCCs, some of these genes were related to cell cycle and signal transduction, such as MCM7, YWHAH, among these, there are 23 genes whose expression tendency consistent with that of cirrhotic liver's. When compared with normal liver, there were 2 genes belong to metallothionein family downregulated in HCCs but upregulated in cirrhotic liver. Conclusions The inactivation of anticancer genes, the abnormality of metabolism related genes and the activation of cell proliferation cycle related genes may have a vital role in HCC. Research into these genes systematically may help to discover new markers of early diagnosis, to guide treatment proposal and to evaluate prognosis better.