Microsporidia constitutes a diverse group of obligate intracellular pathogens that infect a wide range of vertebrate and invertebrate hosts. It has been originally recognized as opportunisti  pathogens of immunocompromised patients. Two species of microsporidia, Encephalitozoon bieneusi and Enterocytozoon intestinalis, are known to infect mainly the gastrointestinal tract of humans. The study was based on the examination of stool samples collected from 100
immunocompetent patients complaining of GIT disturbances attending the Parasitology Department laboratory in the Medical Research Institute, Alexandria, Egypt. Freshly collected stool specimens were examined by modified Trichrome stain MTS (Kokoskin hot method) and immunofluorescent monoclonal antibodies (IFA-MAbs). The results showed that Using MTS, microsporidial spores were detected in 36% of the stool samples examined. Using IFA-MAbs, 60 samples were positive. Microsporidial spores appeared as bright apple green small oval spores with or without vacoule. The agreement between MTS and IFA-MAbs in diagnosing microsporidal infections was moderate. IFA-MAbs differentiated microsporidial infection as 67% E. intestinalis, 6% E. bieneusi and mixed infections in 27% of positive cases.