Objective To screen the differentially expressed genes in esophageal squamous cell cancer (ESCC) and normal tissue of esophageal mucosa in Kazakh. Methods RNA was extracted from the ESCC sections in Kazakh patients, and was amplified to obtain cRNA. The gene expression profiles in ESCC and normal tissue of esophageal mucosa were detected by HG-U133 Plus 2.0 gene chip. The results were analyzed by bioinfor-matics. Results One hundred and seventy differentially expressed genes in ESCC and normal tissue of esophageal mucosa were found, with a difference of more than 10 times in expression levels. Of the 170 genes, 39 were up-regulated (signal log ratio > 3 ) and 131 down-regulated (signal log ratio < - 3). These factors such as cell cycle regulation, apoptosis, cytoskeleton; extracellular matrix, intracellular signal transduction, protein translation and synthesis, and immunological functions were correlated with the genes with abnormal expression. Conclusion The use of oligonucleotide microarray accurately and efficiently screen the 170 target genes in ESCC in Kazakh. It is suggested that these genes may be related to the carcinogenesis and development of ESCC in Kazakh.