Atypical hyperplasia of the endometrium is an entity that needs to be clearly distinguished from other florid hyperplastic states on the one hand and from well-differentiated adenocarcinomas on the other. This may at times be difficult on pure morphological grounds. In this study, DNA ploidy and S-phase fraction of hyperplastic, atypical and cancerous endometrium were evaluated using flow cytometry from paraffin-embedded tissues. In total, 72 cases (24 hyperplastic, 24 atypical and 24 adenocarcinomas) were selected. All hyperplastic endometria showed a diploid stemline, while 2/24 atypical hyperplasias showed aneuploid (Near-diploid) peaks. Both of these cases were severely atypical and one of these, on hysterectomy, showed early invasive carcinoma. There was no significant difference in mean S-phase fractions of hyperplastic vs. atypical endometria. DNA aneuploidy was significantly more common with much higher S-phase fractions in poorly and moderately differentiated carcinomas than in well-differentiated ones. It was concluded that aneuploid (near-diploid) peaks, if ever present in atypical hyperplasias, may indicate an aggressive disease/neoplastic transformation.