A prospective flow cytometric examination of ovarian epithelial tumors was undertaken to further characterize aneuploid (including triploid and tetraploid) tumor cell populations according to expression of ovarian tumor antigen CA125 and to expression of class I (normally present in ovarian epithelium) and class II (normally absent in ovarian epithelium) major histocompatibility complex antigens. Samples from thirty-two of 42 patients (76%) exhibited at least one aneuploid population of tumor cells. Separate analysis of the aneuploid and diploid components of samples with aneuploid populations revealed between-tumor variation: seven of 23 aneuploid populations (30%) were positive for CA125; eight of 22 aneuploid populations (40%) exhibited substantial decreases in major histocompatibility complex class I expression, compared with corresponding diploid components of the same samples; and eight of 22 aneuploid populations (36%) exhibited substantial expression of major histocompatibility complex class II antigens. The frequencies of aneuploid populations and of the foregoing antigen expression categories were independent of tumor cell type, stage, and grade. The significance of these results for prognosis remains to be determined.