To screen the genes associated with esophageal cancer, a cDNA microarray technique was established and used for the analysis of the gene expression profile in human esophageal cancer cell line ECa109. The results showed that 107 (12.08%) genes differentially expressed among 886 target genes were identified between ECa109 cell line and normal human esophageal epithelial cells (HEEC), of which 51 (5.76%) were up-regulated and 56 (6.32%) down-regulated. Two genes were validated by quantitative RT-PCR (Q-RT-PCR) and the results were identical. The RNA amplification technique based-T7 RNA polymerase was established. The gene expression profile revealed better consistency between the amplified samples and those without amplification by T7 RNA polymerase, which provides a method for studying the profile of minute quantities of tumor cells in primary esophageal cancers. And the preliminary study on differential expression gene profile also enables us to have an understanding of the pathogenesis and pathomechanism of esophageal cancer.