Genes expressed in hepatocellular carcinoma (HCC) were analyzed using cDNA microarrays to clarify gene abnormalities in HCC. mRNA was extracted from cancerous and noncancerous tissues of 10 patients with HCC, cDNA labeled with Cy5 and Cy3 fluorescence was prepared, and it was hybridized for each patient with a cDNA microarray consisting of 1,080 elements (930 unique genes). The mRNA expression rate of each element in HCC was evaluated using the level of mRNA expression in noncancerous tissue in each patient as a reference. The expression of 10 genes was enhanced 2 times or more in HCC cancerous tissue compared with noncancerous tissue in 5 or more of the 10 patients. In contrast, 9 genes were expressed at half the level or less in HCC cancerous tissue compared with noncancerous tissue. When hierarchical clustering was performed to identify genes related to clinical phenotypes of the patients, 22 genes showed changes associated with the degree of differentiation of HCC. Thirteen of these genes were transcriptional factors or tissue-specific expression proteins related to cell differentiation or development. Our present analysis clarified a number of genes that characterize HCC. This information based on examination of clinical samples is considered to be useful for clarification of the mechanism of hepatocarcinogenesis and the diagnosis and treatment of HCC.