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To evaluate if morphometric features (mitotic activity index, volume percentage of epithelium, and DNA ploidy) are prognostic markers in borderline ovarian tumors (BOTs). Ninety-three serous and mucinous consecutive BOTs diagnosed between 1989 and 2002 were studied. In all tumors, mitotic activity index, volume percentage of epithelium, and DNA ploidy were determined prospectively. Consecutively, age at diagnosis, calculated tumor volume, International Federation of Gynecology and Obstetrics (FIGO) stage, and treatment by extensive staging were evaluated after a median follow-up of 52 months. Serous BOTs presented at a younger age (P<0.05), with smaller volume (P<0.001), with higher FIGO stage (P<0.001), and were more frequently bilateral (P<0.001) than mucinous BOTs. Patients with serous BOT (P<0.05) and beyond stage Ia (P<0.01) showed worse recurrence-free survival. No prognostic significance could be established for DNA ploidy or morphometry. The previously claimed prognostic power of DNA ploidy and morphometry could not be corroborated in this prospective study and can therefore not be recommended to direct clinical management in BOTs. In contrast, histologic subtype and FIGO stage seem to be stable prognosticators in BOTs.