The reticuloendothelial system (RES) influences the outcome of vascular shock and environmental stress. We describe a procedure that employs flow cytometry and 1 microm fluorescent microspheres (FM) to study RES function. FM (2 x 10(10) beads/kg) were administered via a jugular cannula in Sprague-Dawley rats. After 15 min, blood and tissues were collected and digested in 15% KOH. Phycoerythrin 1 microm beads were added to each sample as an internal standard and analyzed by flow cytometry. FM were preferentially cleared by the spleen, liver and lung. Clearance was confirmed by fluorescent photomicroscopy. Addition of the internal standard to determine accurately aspiration volume enhanced precision. This procedure offers advantages over other RES clearance methods including bacterial, radioactive or carbon clearance assays. Moreover, this method could enhance accuracy, reproducibility and speed of data collection in particulate transport studies that are based on manual microscopic scanning and FM counting.