Ubiquitous in nature, members of the Coccidia and Microsporida are being reported with increasing frequency in the immunocompromised as well as the immunocompetent population. These protozoans are primarily waterborne, but foodborne disease has also been reported. These organisms are responsible for acute, as well as protracted, cases of watery diarrhea with various other related sequelae. The Coccidia includes three genera--Cryptospridium, Isospora, and Cyclospora. The latter two are of lesser importance in terms of morbidity and mortality. The Microsporida includes genera (Enterocytozoon, Encephalitozoon) only recently recognized as important agents of disease. Unlike the Coccidia, these organisms are more restricted to the immunocompromised population. Increased incidence and numbers of patients with prolonged diarrhea due to these forms indicate the need for increased clinical vigilance with regard to prevention, diagnosis, and treatment.