Apoptotic membrane microparticles (MMPs) derived from dying cells of multiple cell origins are highly immunostimulatory and are indicative of global immune activation and cell death in a variety of diseases. In this study, we developed a flow cytometric bead assay to quantify annexin-V + apoptotic (MMPs) in plasma from humans and rhesus macaques. With a combination of flow cytometry and pan-fluorescent beads, MMPs were enumerated in plasma specimens by adding a constant ratio of beads to initial fluid volumes and then calculating MMP/mL based on MMP-to-bead ratios. Using this straightforward assay, we found that circulating MMP quantifications were highly reproducible and similar in number between normal rhesus macaques and humans subjects. However, MMPs increased two- to threefold during HIV and simian immunodeficiency virus (SIV) infections and were positively associated with T cell immune activation. Collectively, we present a rapid bead-based assay for both humans and macaque models to quantify MMPs that could be an instigator and predictor of immune activation, which is a primary source of HIV/SIV disease.