Abstract: Objective Screening gene expression profiling from hypopharyngeal squamous cell carcinoma of different chemotherapy sensitivity and explore the possibility to predict the chemotherapy sensitivity by gene expression profiling. Methods Total RNA was isolated from four samples from chemotherapy sensitive and resistant hypopharyngeal squamous cell carcinoma respectively.Then synthesized into cDNA and cRNA in vitro in turns.The cRNA probe,after biotin-labelled and fragmented,hybridized with human gene micro-array.The hybridization signal was scanned by the Gene Array scanner,analyzed by GCOS 4.0 statistic software after normalization.The Signal Log Ratio≥1 and change P-value≤0.05 were standard for identified significant difference genes.The gene was sorted out according to bio-process and function. Results Different gene expression profiling consisting of 119 genes was screened out.Among them,65 genes was up-regulated and 54 genes down-regulated,aberrant expressing genes were relative to signal transduction(STAT3),cell cycle(CCND1,TCF7L1),apoptosis (FADD),cell adhesion(MUC4,cadherin 11,ICAM2),enzyme(AKAP7,CDKN2A,MMP2) and so on.Signaling pathway of endepidermis growth factor receptor,TNF-β and STATs was dysfunction in the sensitive. Conclusion Hypopharyngeal squamous cell carcinoma of sensitive and resistant to chemotherapy had different gene expression profiling.It's possible to assess the sensitivity of hypopharyngeal squamous cell carcinoma before chemotherapy by gene expression profiling.