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Objective: To compare the whole gene expression profile between EBV positive gastric carcinoma cell lines and EBV negative ones. Methods: Agilent Human Whole Genome Expression Profiling chips were used to detect and analyze the whole gene expression profile of EBVa GC in 3 EBV positive and 3 negative gastric carcinoma cell lines. Six candidate genes were chosen for real-time PCR validation. Results: Heat map and matrix plot analysis found distinctly different expression profile between EBV positive gastric carcinoma cell lines and negative gastric carcinoma cell lines. These tumor associated genes involve many biological process. The expression trend of 6 genes for further verification was consistent with the microarray. Conclusion: Our study suggests that EBV infection may change the expression of tumor associated genes, which may play roles in the formation, development and prognosis of EBVa GC.The differentially-expressed genes involve many biological processes, suggesting that many genes and their mutations play roles in the formation of EBVa GC. [ABSTRACT FROM AUTHOR]