Increasing isolation of Cryptosporidium, Cyclospora, and microsporidia from immunocompromised patients with severe diarrhea has prompted study of these organisms. Only recently recognized as human pathogens, they have also been associated with several waterborne outbreaks of diarrhea in immunocompetent individuals. Cryptosporidium and Cyclospora have been shown to be transmitted through fecally contaminated food and water. The mode of transmission for microsporidia is still unclear. While the life cycle and pathogenesis of Cryptosporidium are beginning to be understood, the microsporidia and Cyclospora are less well elucidated. The laboratory diagnosis of these protozoa is difficult. The routine ova and parasites screen does not include screening for them. Many microscopic methods, including wet mounts, modified acid-fast and trichrome stains, and immunofluorescence methods have been shown to be effective screening methods in the hands of experienced microscopists. Enzyme immunoassay and polymerase chain reaction methods also show promise. The proper identification of these pathogens rests with well-trained laboratory personnel. As appropriate treatment differs for each genus, communication between the laboratory and the physician is vital to the recovery of the patient.