To study DNA topoisomerase IIα (Topo-IIα) and -β expression and regulation in human ovarian cancer, 15 ovarian tumour samples were investigated. To compare different levels of expression, the samples were screened for topo IIα and -β mRNA with Northern blotting and a quantitative reverse transcriptase polymerase chain reaction (RT-PCR) assay for Topo-IIα mRNA. Additionally, protein levels were determined with Western blotting and topoisomerase II activity levels with the decatenation assay. The results obtained were compared with each other and with the tumour volume index of the samples. In tumours with a tumour volume index ≥ 50%, the mRNA levels (as determined by Northern blotting) and protein levels for each isozyme were in accordance. Additionally, correlations were found between Topo-IIα RT-PCR data and Topo-IIα Northern blot results, and between Topo-IIα RT-PCR data and Topo-IIα protein levels. Interestingly, Topo-IIβ protein levels correlated better with Topo-II activity than Topo-IIα protein levels. In eight ovarian cystadenoma samples, no Topo-IIα protein could be found. In only three out of eight of these cystadenomas, Topo-IIβ protein could be detected. These findings suggest that Topo-IIα and Topo-IIβ protein levels are up-regulated in ovarian cancer and may indicate that Topo-IIβ is an interesting target for chemotherapy in ovarian tumours. © 1999 Cancer Research Campaign