The aim of this study was systematic investigation of the differentially expressed genes during carcinogenesis in hepatocellular carcinoma (HCC) using cDNA microarray technology. The differentially expressed genes between 22 fresh HCC tissues and para-carcerous liver tissues (PCLT) were displayed using cDNA microarray technology. The result was verified by the reverse transcriptase polymerase chain reaction. Among the 8,464 human genes, 507 (5.99%) genes were expressed differentially at the mRNA levels between HCC and PCLT. Two hundred (2.36%) genes were down-regulated, whereas 307 (3.63%) genes were up-regulated. The mRNA expression levels of RhoC and protocadherin LKC detected by reverse transcription polymerase chain reaction (RT-PCR) were consistent with the microarray experiment. This study describes a gene expression profiling of HCC, which provides an extensive list of potential molecular markers for early diagnosis and molecular targets for the development of drugs to treat patients with primary HCC.