This unit describes a system for the automated high-throughput analysis of cell cytotoxicity in 96-well and 384-well microplates. Discrete cell cultures are analyzed at rates of 40/min (approximately 2.5 min/96 wells, approximately 10 min/384 wells) and cytotoxicity is quantified on the basis of a combination of propidium iodide (PI) fluorescence analysis and cell counting performed by the flow cytometer. Only 2 microl is aspirated from a culture for analysis so that assays can be performed in small volumes to minimize reagent cost and usage.