Objective:To investigate the gene expression profiles of squamous esophageal cancer carcinoma(ESCC). Methods:The cDNA retro-transcribed from both 3 cases(groupⅠ) and 6 cases(groupⅡ),which consisted of equal quantity of both squamous esophageal cancer tissues and adjacent normal tissues,were labelled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with a piece of Biostar H-140s single dot human whole gene chip. It was scanned by scanarray 4 000 instrument. The acquired image was analyzed by GenePix Pro 3.0 software. Results:There were 1 855 genes in groupⅠ and 613 genes in the groupⅡ,respectively,whose Cy5/Cy3 ratio was greater than 2.0 or less than 0.5. Furthermore, there were 60 genes, whose Cy5/Cy3 ratio wasgreater than 2.5 or less than 0.25 simultaneously in bothⅠgroup and Ⅱ group, including 30 ESTs in GenBankTM. There are 26 genes that has not been reported relating to squamous esophageal cancer,except 4 genes of epithelial membrane protein 1(EMP1),secreted phosphoprotein 1(SPP1),ubiquitin-conjugating enzyme E2C(UBE2C) and retinoblastoma-like 2 (p130) (RBL2). Conclusion:Microarray may play important roles in exploring the gene change in ESCC with and without family history, to illustrate the mechanism on the developement of ESCC.