Photosynthetic rates of phytoplankton were significantly lower after analysis by flow cytometry (FCM) than before. Exposure to the laser beam during the sorting process caused significant physiological damage. The cellular content of a radiolabel accumulated prior to FCM was not affected by FCM. Although it may not be possible to use FCM to preconcentrate cells for further physiological studies, samples may be incubated with stable or radioactive isotopes and then analyzed by FCM.