Loss of chromosome Y has been reported in gastric cancer cells together with other chromosomal abnormalities. We noted loss of chromosome Y and near-diploid karyotypes in five cases of gastric adenocarcinoma, but DNA flow cytometry performed on fresh tumor tissue showed aneuploid peaks in four of them. Our findings suggest that loss of the Y chromosome in gastric cancer probably reflects the karyotype of a subpopulation of stromal cells and not a neoplasia-related chromosomal aberration.