The use of flow cytometry as a rapid, high-throughput diagnostic tool for the analysis of ions is described. Monodisperse, uniform microspheres, which obey bulk optode theory and are governed by bulk extraction processes rather than surface phenomena, were prepared under mild, nonreactive conditions using a sonic stream particle casting apparatus. As an initial example demonstrating the utility of this approach, microspheres that contained a H+-selective fluorescent chromoionophore (ETH 5294), a cation-exchanger (NaTFPB), and either a highly sodium-selective (sodium ionophore X) or a potassium-selective ionophore (BME-44) were prepared. Separate solution analysis of sodium- and potassium-selective microspheres resulted in the generation of functional response curves using peak channel fluorescence intensities. The selectivity observed for both types of particles is sufficient for the clinical determination of Na+ and K+. Furthermore, sodium- and potassium-selective microspheres were analyzed in parallel using sodium sample solutions, resulting in the successful determination of sodium ion concentrations and providing important information about the selectivity of the potassium-selective sensors over sodium. This work demonstrates the potential applicability of flow cytometry as a means for developing multiplexed, rapid, high-throughput analyses for clinically relevant ions.