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Background The use of patients' own cancer cells for in vitro selection of the most promising treatment is an attractive concept in personalized medicine. Human carcinoma cells from malignant effusions (MEs) are well suited for this purpose since they have already adapted to the liquid environment in the patient and are not enclosed by stromal cell compartments. Aim of this study was the establishment of a consistent approach for the in-vitro ex-vivo culture of MEs and the comprehensive analysis of the effect of chemotherapeutic as well as targeted drugs. Methods MEs from patients with lung or breast cancer were selected for this study. After morphological and molecular characterization, epithelial cells were cultured in cell culture medium supplemented with 30% of patient derived sterile filtered effusion supernatant. Growth characteristics were monitored in real-time using the xCelligence system. MEs were treated with targeted therapeutics according to their genomic profile or with chemotherapeutics based on the recommendation by the oncologist. Results We have developed a reliable system for the ex-vivo culture of MEs and the application of drug tests in-vitro. The use of an enrichment system for epithelial cells allowed for culturing of effusions with only moderate tumor cell content. Experiments using drugs revealed dose-dependent effects and specific growth inhibitory effects of targeted therapeutics, such as Crizotinib and Erlotinib. Conclusions In this study, we show that cancer cells from patient derived MEs can be cultured and treated in-vitro. Based on our developed setup, these MEs can be genomically characterized by whole genome approaches in order to identify genomic vulnerabilities and then subjected to growth tests by using the respective targeted drugs. This approach could be an important step towards personalized healthcare, at least for patients with malignant effusions. Citation Format: Christian Ruiz, Tatjana Vlajnic, Leila Arabi, Sina Wyttenbach, Betty Baschiera, Sacha Rothschild, Stefan Kustermann, Alfred Zippelius, Adrian Roth, Lukas Bubendorf. The use of patient derived malignant effusions as in vitro models for a personalized healthcare-approach in anticancer therapy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4681. doi:10.1158/1538-7445.AM2014-4681