To screen the differential expression genes of nasopharyngeal carcinoma(NPC), the cDNA microarray technique was employed to analyze the changes of gene expressions with GenMAPP. Total RNA was extracted from NPC and normal nasopharyngeal epithelium tissue respectively. Reverse transcription was performed and cDNA probe was random-prime labeled with 33P-dATP and hybridized with the cDNA microarray membrane containing 16 150 genes and ESTs. The hybridized result was confirmed by RT-PCR analysis. The results suggested that 339 genes were differentially expressed over two fold, in which 160 genes were up-regulated and 179 genes were down-regulated in NPC. These genes were involved in cell proliferation, gene transcription, apoptosis, signal transduction, DNA damage and repair, tumor differentiation and metastasis, cell cycle, and so on. Therefore, the data suggested that some genes play a critical role in NPC, and provided an important clue to elucidate the mechanism of these genes.