The flow cytometer is unique among biomedical analysis instruments in its ability to make multiple correlated optical measurements on individual cells or particles at high rates. Moreover, an ever-expanding arsenal of fluorescent probes enables the modern flow cytometer to quantify a large and growing diversity of cell-associated macromolecules and physiological processes. Modern flow cytometers have achieved such a level of sophistication and reliability that unattended operation by automated systems is a practical reality. From its inception, flow cytometry has been in the vanguard of automation in cytological analysis. One of the most powerful automated features is cell sorting, an operation in which highly purified subsets of cells or particles are isolated from heterogeneous source populations on the basis of a targeted, multiparameter phenotype. The method most widely used for sorting today, which is based on electrostatic deflection of charged droplets, was developed over 30 years ago and led to commercial flow cytometers that were capable of sorting cells at rates of hundreds of cells per second. Influenced by the need of the Human Genome Project for efficient isolation of purified chromosomes, a high-speed chromosome flow sorter was developed and patented in 1982 that increased sort rates to tens of thousands of events per second (13). Commercial systems subsequently became available in the 1990s that permitted sorting of cells at such high rates (www.bdbiosciences.com; www.dakocytomation. com). Thus, since the initial development of the technology, the throughput of automated cell sorting has increased by nearly two orders of magnitude. In single cell analysis and sorting, throughput is determined by the rate at which the flow cytometer can process individual cells as they pass single file through the point of detection. Another aspect of flow cytometer throughput concerns the rate at which the flow cytometer can sequentially process multiple discreet collections of cells. This component of throughput will be important, for example, in the screening of collections of test compounds for their effects on bulk populations of cells. This is of particular relevance for modern drug discovery, in which there is a need to test cellular targets against millions of potentially valuable compounds that may bind cellular receptors to effect clinically therapeutic cellular responses.