Microsporidial pathogens, including members of the genus Enterocytozoon (E. bienusi) and Encephalitazoon (E. intestinalis, E. cuniculi, E. hellem), cause a variety of infections in man including gastroenteritis, keraconjunctivitis, respiratory tract infections, hepatitis, peritonitis, sinusitis, nephritis, prostatitis, and encephalitis (Wittner and Weiss, 1999). These organisms are environmentally resilient and difficult to remove using conventional water treatment practices (Harrington et al., 2001). Although there have been no documented waterborne outbreaks attributed to these protozoa, transmission via drinking water is possible. Detection methods for these organisms are nonexistent, and laboratory identification of microsporidia-contaminated environmental samples may prove to be even more difficult than Cryptosporidium due to the small size of the microorganism. The overall objective of this study is to develop a strategy for the recovery and identification of pathogenic microsporidia from natural water samples. The study describes the development and optimization of a newly-modified continuous flow centrifuge and flow cytometry for detection of waterborne microsporidia. Includes 6 references.