To investigate the expression profile of gastric adenocarcinoma, cDNA array experiments were performed using Atlas Human Cancer 1.2 K Array (Clontech Laboratories, Palo Alto, CA) on nine xenografted and two primary gastric cancer samples. The expression of the tumor samples was compared to that of two normal gastric epithelial tissues. The expression pattern of the primary tumors was similar to that of xenografted tumors. The up-regulated genes had expression ratios ranging from 2.5 to 16, whereas the down-regulated genes had a range from -2.5 to -16. No variation in gene expression was detected in the analysis of the xenografted tumors versus the primary tumors, indicating that the xenografts represented the primary tumors well. Thirty-eight genes showed altered gene expression in 5 or more samples (>45%). Thirty-one genes were up-regulated and seven genes were down-regulated. The most abundantly up-regulated genes (ratio >5) included genes such as S100A4, CDK4, MMP14 and beta catenin. The GIF was markedly down-regulated (ratio < -10). To confirm our findings, six genes (three up- and three down-regulated) were selected for semi-quantitative RT-PCR analysis. The RT-PCR results were consistent with the array findings. Our approach revealed that several genes are abnormally expressed in gastric cancer and found that genes known to interact in several common molecular pathway(s) were consistently altered.