AbstractAlthough flow cytometry has the powerful ability to rapidly screen large collections of cells, the technology has yet to be efficiently applied to large‐scale screening operations involving multiple discrete suspensions. High‐throughput flow cytometry would be beneficial to many areas of biological investigation, such as modern drug discovery, which involves testing of cellular targets against millions of potentially valuable compounds. The authors have developed a flow injection analysis approach to automated sample handling in which individual sample suspensions are sequentially inserted as plugs of precisely defined volumes into a flowing fluid which delivers them to the laser beam. The unit describes the basic elements and concepts of this plug flow system and discusses representative applications.