Aim: To identify tumor-associated genes by constructing transcription profiles of pure hepatocellular carcinoma (HCC) tissues and normal liver tissues with the combination of laser capture microdissection and microarray. Methods: HCC cells and normal liver cells from resection samples of 4 patients were laser capture microdissected. Micro-RNA was isolated from them for linear amplification then cRNA was tested with whole genome microarray. Differentially expressed genes were screened. Results: The quality control of this technique was satisfactory with RNA Integrity Number>7, A260/A280 ratio for cRNA measurement=2.0~2.1 and good pictures for microarray. Compared with normal liver tissues, HCC had 1361 differentially expressed genes, with 607 being up-regulated and 754 being down-regulated genes respectively. Among the top ten ranked up-and down-regulated genes (total 20), 5 genes were known as HCC differentially expressed genes, 11, known as other tumors expressed genes previously.