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<p>Abstract</p> <p>Background</p> <p>Esophageal squamous cell carcinoma (ESCC) is one of the most malignant tumors and typically presents at an advanced and rapidly fatal stage. To better understand the role of genetics in the etiology and prevention of ESCC and to identify potential susceptibility genes as well as early detection markers, we previously compared tumor and matched normal tissues from ESCC patients from a high-risk area of China using cDNA expression microarrays and identified 41 differentially-expressed genes (13 over-expressed and 28 under-expressed).</p> <p>Methods</p> <p>In the current study, we validated and quantitated differential mRNA expression in a sample of nine of these 41 genes, including four that were over-expressed (<it>SPARC</it>, <it>FADD</it>, <it>Fascin</it>, <it>COL7A1</it>), and five that were under-expressed (<it>CK4</it>, <it>TGM3</it>, <it>ECM1</it>, <it>PPL</it>, <it>EVPL</it>), in 75 new ESCC patients using quantitative Real-time RT-PCR and the 2^-ΔΔCTmethod to examine both tumor and matched normal tissue. In addition, we examined expression patterns for these genes by selected demographic and clinical characteristics.</p> <p>Results</p> <p>Four previously over-expressed (tumor ≥2-fold normal) genes were all increased in the majority of new ESCC patients: <it>SPARC </it>was increased in 71% of patients, <it>Fascin </it>in 70%, <it>FADD </it>in 63%, and <it>COL7A1 </it>in 57%. Five previously under-expressed (tumor ≤0.5-fold normal) genes similarly showed decreased mRNA expression in two-thirds or more of patients: <it>CK4 </it>was decreased in 83% of patients, <it>TGM3 </it>in 77%, <it>ECM1 </it>in 73%, and <it>PPL </it>and <it>EVPL </it>in 67% each. In subset analyses, associations with age (for <it>COL7A1</it>), family history (for <it>PPL </it>and <it>ECM1</it>), and alcohol use (for <it>SPARC </it>and <it>Fascin</it>) were also noted.</p> <p>Conclusion</p> <p>These data indicate that these nine genes have consistent differential mRNA expression, validating results of our previous cDNA array results, and affirming their potential role in the early detection of ESCC.</p>