Chromosomal numerical abnormality (CNA) is one of the distinct characteristics of human cancers, though the mechanisms and tumor specificity of this phenomenon have not been adequately analyzed. Recently, we developed a new sensitive fluorescence in situ hybridization (FISH) method that involves short-term microwave (MW) treatment for hybridization. In this study, we applied this modified FISH technique to investigate the CNA of 60 gastric cancer cases with a panel of 18 chromosome-specific alpha-satellite probes (for chromosome 1-4, 6-12, 15-18, 20, X, and Y) and region-specific probes (c-myc, p53, and Her-2/neu) to enumerate the respective chromosome numbers in interphase nuclei of formalin-fixed paraffin-embedded sections. The numerical aberrations of chromosome 1, 3, 8, 17, 20, and X were frequent regardless of histologic types, whereas aberrations of chromosomes 10, 15, and 18 occurred less frequently (p<0.001). From a histopathological standpoint, the mucocellular type of carcinoma had stable CNA in comparison with the tubular type of carcinoma (21.7+/-9.63% vs. 58.3+/-12.32%, p<0.001) and, of note, there was less extensive CNA in female cases. A dramatic difference in patient outcome was detected according to the involvement of chromosomes 3, 10, 11, 12, 17, and Y; cases with CNA of these chromosomes had a worse prognosis (p<0.001). A two-step analysis of the CNA of 6 chromosomes and locus specific gene abnormalities successfully divided gastric cancer cases into those with a good outcome and those with a poor outcome. This analysis allows one to more accurately predict prognosis than by using a simple classification based on conventional clinicopathological diagnosis.