Ovarian carcinoma (OC), primary peritoneal carcinoma (PPC) and malignant mesothelioma (MM) are all highly aggressive tumors that share common morphological features in addition to being histogenetically related. It is of great interest to investigate the underlying molecular differences amongst these tumor types. The identification of differential gene expression signatures has the potential to serve as biomarkers, which can be used for diagnosis and prognosis of these tumors. This study examines the gene expression levels of RAB25, PRAME and EHF, in addition to RAB25 protein expression levels, in large sample material consisting of primary OC, OC/PPC effusions and MM effusions. The results showed higher expression of RAB25, PRAME and EHF mRNA in OC/PPC effusions compared to MM effusions, in addition to significantly higher expression of EHF mRNA primary OC compared to OC/PPC effusions. The study also revealed pronounced differences in RAB25 protein expression between OC/PPC effusions and MM effusions, along with significantly higher RAB25 protein expression in histological grade 3 compared to grade 1-2 within the OC/PPC effusions. Another result generated in this study was that there is a significantly higher expression of EHF mRNA in the pre-chemotherapy OC/PPC effusions, and this upregulation proved to be correlated with poor progression free survival survival, also independent in COX multivariate analysis.