Gastric cancer is one of the most common malignancies in Korea, but the predominant molecular event underlying gastric carcinogenesis remain unknown. Recently, DNA microarray technology has enabled the comprehensive analysis of gene expression level, and as such has yielded great insight into the molecular nature of cancer, However, despite the powerful approach of this techniques, the technical artifacts and/or bias in applied array platform limited the liability of resultant tens of thousand data points from microarray experiments. Therefore, we applied two different any platforms, such as olignucleotide microarray and cDNA microarray, to identify gastric cancer related large-scale molecular signature of the same human specimens. When thirty sets of matched human gastric cancer and normal tissues subjected to oligonucleotide microarray, total 623 genes were resulted as differently expressed genes in gastric cancer compared to normal tissues, and 252 genes for cDNA microarray analysis. In addition, forty three outlier genes which reflect the characteristic expression signature of gastric cancer beyond array platform and analytical protocol was recapitulated from two different expression profile. In conclusion, we were able to identify robust large-scale molecular changes in gastric cancer by applying two different platform of DNA microarray, this may facilitate to understand molecular carcinogenesis of gastric cancer.