Microsporidia are intracellular-living spore-forming protozoa, classified into more than 50 genera and over 600 species. They infect various animals and nonvertebrates. Some nonvertebrate hosts are mosquitos, honey bees, fish, and grasshoppers. In humans, clinical disease has only recently been noticed, and only in persons with AIDS. Here, the predominant species is Enterocytozoon bieneusi, which primarily infects epithelial cells of the small intestine (producing diarrhea), but also epithelial cells from the biliary tract, colon, pancreas, liver, eye, and probably other tissues and organs. The organism produces spores that are gram-positive, are 1.5 by 0.9 microns in size, and can be found inside or outside infected epithelial cells. About 50% of patients with AIDS develop chronic diarrhea; about 50% of these cases have no known cause; and about 30% of those with previously unknown etiology are now thought to be caused by microsporidia. Those patients with Microsporidium-induced diarrhea usually have CD4 lymphocyte counts less than 200. One study was able to find intracellular microsporidia in some AIDS patients without diarrhea.

Diagnosis can be made by electron micrography of infected tissue epithelial cells; this technique also identifies microsporidial spores. Gram stain of tissues may show the spores. One report described a modification of the standard trichrome stain used for O&P permanent slides that can be applied to nonconcentrated stool specimens or duodenal aspirates.