Regional differences in DNA ploidy of gastrointestinal carcinomas were investigated by flow cytometric (FCM) analysis of multiple samples taken from different sites of each tumor of 42 patients. The overall incidence of DNA aneuploidy in the 42 cases examined was 80%, and the DNA index (DI) ranged from 0.825 to 2.170. However, intratumoral differences in DNA ploidy were observed in six of 15 cases (40.0%) of gastric carcinoma, whereas intratumoral differences in DNA ploidy were observed in only two of 27 cases (7.4%) of colorectal carcinoma. Therefore, to accurately determine DNA ploidy, one must analyze multiple samples from the tumor specimen (especially in gastric carcinomas) because cases exist where subpopulations with DNA aneuploidy are detected only at limited sites within the same tumor. The exact mechanisms responsible for the regional differences in DNA ploidy are not yet clear, although some hypotheses have been presented.