Flow cytometry has been used to rapidly and reliably measure DNA content in malignant tumor cells. Although several studies have suggested that DNA ploidy is a powerful predictor of survival in women with epithelial ovarian cancer, few have determined the usefulness of this procedure in women with borderline tumors. Using data from a population-based tumor registry covering all of western Washington State, women who died prior to 1992 as a consequence of developing a borderline ovarian tumor between 1975 and 1986 were compared to an age, histology, and histologic stage-matched sample of women with the same diagnosis still living after at least 5 years of follow-up. Flow cytometry analysis was conducted using sections of tumor from the original paraffin blocks. Overall, 25% of the women who died and 24% of those still alive had aneuploid DNA tumors (odds ratio = 1.2, 95% CI = 0.3-4.9). This lack of association stands in contrast to the strong relationship of aneuploid status to mortality in an earlier, similarly designed, study of borderline ovarian tumors. We believe that additional studies are required prior to concluding that the clinical course of women with borderline tumors can be predicted by the ploidy status of their tumor's DNA.