Differential diagnostics of borderline ovarian tumours and ovarian carcinomas is generally based on morphological criteria, which are not always sufficient for final diagnosis. Therefore, we investigated the practical diagnostic application of the CAS200 image analyzer and new ploidy-related parameters in a series of 68 borderline tumours and 42 low-grade carcinomas of the ovary. Highly significant differences between borderline and malignant lesions were found for the percentage of diploid cells (p = 0.0001), the percentage of aneuploid cells between 4c and 8c (p = 0.0001), the percentage of octaploid cells (p = 0.0001), as well as for the 5c exceeding rate (p = 0.0001). The difference concerning the ratio of tetraploid cells also reached the level of significance (p = 0.0320). We suggest that new ploidy-related parameters evaluated by the CAS200 image analyzer can be helpful in ovarian lesions with unclear morphology.