Microparticles, found in all body fluids including peripheral blood, are important elements that regulate cellular interactions under both physiological and pathological conditions. They play an important role in blood clot formation and increased cell aggregation. However, little is known about the components of the microparticles and their mechanism of action. A method to quantify and assess the underlying mechanism of action of microparticles in pathologies is therefore desirable. We present a specific method to isolate cell-derived microparticles from malignant effusions using annexin V-coated magnetic microbeads. The microparticles can be detected by flow cytometry. Our results show that the microparticles can be isolated with >80% specificity when bound to annexin V-coated magnetic beads, which was originally developed for the detection of apoptotic cells. We also show that the isolated microparticles were still functionally active and can be used for further analysis. Thus, our method enables isolation as well as structural and functional characterisation of the microparticles which are produced in numerous patho-physiological situations. This should help gain a deeper insight into various disease situations, which in turn should pave the way for the development of novel drugs and specific therapy strategies.