AbstractSeveral protozoa have emerged as the major opportunistic infections and cause of death in patients with acquired immunodeficiency syndrome (AIDS).Pneumocystis cariniipneumonia is the leading cause of death in AIDS patients. Electron microscopy (EM) usually shows numerous trophozoites and cysts ofPneumocystisfilling up the entire alveolar space, while only cysts are seen under the light microscope. The focal thickening of cyst wall ofPneumocystis, as demonstrated by EM and manifested as a “parentheses” shaped structure with silver stain, serves as a diagnostic marker forPneumocystis.Freeze‐fracture EM has demonstrated the intimate contact betweenPneumocystistrophozoites and the type I pneumocytes, which may contribute to the alveolar‐capillary block, leading to severe respiratory distress. However, EM is seldom needed for the diagnosis of this infection.Toxoplasmaencephalitis, which is an unusual clinical manifestation in cases of toxoplasmosis reported previously, has become a common complication and one of the major causes of death in patients with AIDS. Because subclinical infection byToxoplasmais common, serologic tests usually offer no definite answers as to whether the infection is acute or chronic, active or past. The small size and its non‐specificity in both morphology and tissue affinity make light microscopic diagnosis of toxoplasmosis difficult. Only immunologic staining, such as immunoperoxidase and immunofluorescence, can help to achieve a definite positive identification of the organism. When special antibodies or facility for such staining is not available, EM is the final resort for identifyingToxoplasmaby showing the apical complex with the characteristic sausageshaped rhoptries.Cryptosporidiosis, practically unknown before the AIDS outbreak, has become one of the most common intestinal protozoa in both immunocompromised and immunocompetent patients. The protracted and sometimes fatal course of cryptosporidiosis in immunocompromised patients can be explained by the presence of autoinfective oocysts (thin‐walled oocysts), as detected by EM, and by recycling of first‐generation schizonts observed experimentally. While diagnosis of cryptosporidiosis can be made by detection of oocysts in stools in most cases, EM is still the last resort for a definitive identification ofCryptosporidiumspecies.While the incidence of isosporiasis is still low, it has been found more frequently in patients with AIDS than in the general population. The parasite,Isospora belli, being a coccidian as is theCryptosporidiumspecies, is similar to the latter in its life cycle and clinical manifestations. However, the morphology of its diagnostic stage, the oocyst, is quite different from Cryptosporidium and it is much larger than the latter. The oocyst of Isospora belli, usually containing one sporoblast, can be detected by light microscopy in stools.Microsporidiosis, having been known only recently, is also relatively common in immunocompromised patients, including four patients with AIDS. Although this protozoan can be detected by light microscopy and its polar granules, identified by the periodic acid‐Schiff or methenamine silver stain, are characteristic, a definitive diagnosis of microsporidiosis stil