Recent advances in cDNA microarray techniques have enabled us to study the expression of many genes simultaneously. As gastric cancer remains one of the most common cancers in Japan, we studied gene expression profiles in gastric cancer by cDNA microarray analysis to determine if it would be clinically useful. We demonstrated two points. First, cDNA microarray might be useful as a prognostic indicator. However, there remain several important problems to be solved and these are discussed. Second, laser microdissection plus cDNA microarray might be useful in determining the specific genes that correlate to cancer metastasis or histological subtype. We review the pros and cons for cDNA microarray analysis in the context of gastric cancer.