Infection and thromboembolism remain significant complications associated with ventricular assist device (VAD) support, including the newer rotary VADs, limiting wider adoption of this promising technology. These complications persist in spite of extensive preclinical testing in large animal models. The amount of biocompatibility information collected during preclinical trials is limited due to a lack of available assays. We thus developed three flow cytometric assays to measure leukocyte-platelet aggregates and monocyte tissue factor expression and applied them to 26 bovines implanted with two types of rotary VADs. All animals displayed low levels of circulating aggregates and monocytes expressing tissue factor prior to device implant. The assay values significantly increased following VAD implant, then usually declined to a lower, yet significantly elevated versus baseline, level indicative of ongoing inflammation. The implementation of more robust biocompatibility assays for the evaluation of cardiovascular device performance and modification might ultimately contribute to the development of safer artificial organs.