The CTNNB1 gene and its product beta-catenin, a regulator of the Wnt signalling pathway, is often mutated and deregulated in human malignancies. Down stream targets of the Wnt signalling pathway are linked to genomic instability. In this study, the impact of beta-catenin expression on genomic instability in ovarian carcinoma, as determined by DNA ploidy, was investigated. Expression of beta-catenin was examined by immunohistochemistry in 253 ovarian carcinomas. The results were related to genomic instability and clinicopathological features of the patients. Membrane associated staining of beta-catenin was detected in nearly all cases with no correlation to clinical parameters. Most of the samples also had cytoplasmic (84%), while only 13% had nuclear beta-catenin localisation. A significant association between beta-catenin expression (cytoplasmic and nuclear) and histological subtype and degree of differentiation was observed. Nuclear beta-catenin was almost exclusively present in endometroid carcinomas. 53% of all endometroid tumours were positive for nuclear beta-catenin expression (P<0.0001). Mucinous carcinomas had the highest degree of cytoplasmic beta-catenin expression (92%), followed by endometroid (92%), mixed (90%), serous (82%), unclassified adenocarcinomas (81%), carcinomas clear cell and (70%), (P=0.01). Tumours with differentiation grade 1 (16%) and 2 (24%) had higher nuclear beta-catenin expression than grade 3 and clear cell carcinomas (6%) (P=0.012). Better prognostic outcome was found for patients with nuclear beta-catenin localisation as compared to the cases without (P=0.027). In conclusion, the study showed no correlation between beta-catenin expression in ovarian carcinoma and FIGO stage and genomic instability as determined by DNA ploidy status. However, nuclear beta-catenin expression was strongly associated with endometroid histological subtype. Finally, in ovarian cancer, although beta-catenin staining seems to be of prognostic importance with respect to nuclear staining in univariate analysis, only DNA ploidy status, histological grade and FIGO staging were of independent prognostic significance in multivariate analysis.