Abstract: Objective To investigate the difference of gene expression profile in esophageal squamous cell carcinoma tissues (ESCC) and their adjacent almost normal tissues. Methods The cDNA retro–transcribed from 3 cases mRNA，which consisted of equal quantity of both ESCC and adjacent almost normal tissues，was labeled with Cy5 and Cy3 fluorescence as a probes. The mixed probes were hybridized with a piece of Biostar H-140s single dot human whole gene chip. The fluorescent signal was scanned by scanarray 4 000 instrument. The acquired image was analyzed by Genepix Pro 3.0 software. Results In 1 855 genes,whose Cy5/Cy3 ratios were greater than 2 or less than 0.5. There were 844 expressed sequence tags(ESTs), including 378 down-regulated genes and 466 up-regulated genes.On the other hand, among the 1 011 genes, which were acquired from genebank, included 560 down-regulated genes and 451 up-regulated genes.In the meantime, compared with the profiles from 6 cases of ESCC with family history,there were 8 of the 1 011 genes identical to the Genebank,and the expression of the 8 genes were same as the report as well. Conclusion Using the microarray to detect the difference of gene expression profiles might be of benefit to rapid select the relative genes of the esophageal carcinoma. There are lots of genes involved in the progression of ESCC.