Objectives: Objective of this work is to provide a new and more sensitive method based on RT-qPCR (quantitative polymerase chain reaction) for biocompatibility testing in order to facilitate further improvements of dialysis filter devices. Need for improved biocompatibility is given by the clinical observation that dialysis patients have increased risk of cardiovascular disease that is suspected to be influenced by the foreign surface contact. Although there exist a couple of methods to measure biocompatibility, these methods are not sensitive enough to differentiate biocompatibility of modern filter devices and consequently these methods are not suited to guide future developments. Methods: The method is a two-step in vitro process. The first part is the exposure of human blood in parallel to two dialysis filter devices. The second part is the quantitative analysis of the activation level of the leukocyte cell population. The activation level is quantified by the amount of mRNA of a specified set of inflammatory markers by real-time quantitative PCR. Additional information is obtained by FACS analysis of surface marker proteins. Results: RT-qPCR analysis of inflammatory markers in human blood showed that exposure of blood to different filter devices resulted in different leukocyte activation levels. Particularly early inflammatory markers like TNF- alpha and IL-1 beta revealed statistically significant differences between filter devices. Though physical and chemical analysis of the filter materials showed differences in filter materials, no single parameter could be correlated to increased leukocyte activation. Conclusions: A new method based on RT-qPCR could be established for biocompatibility testing of modern dialysis filter devices. The method allows in vitro characterization of inflammatory processes that are caused by foreign surface contact and are suspected to be clinically relevant for cardiovascular complications. Moreover, the method showed differences in leukocyte activation between commercial dialysis filters and is therefore suited to guide further improvements in biocompatibility.