There are several protozoan infections that cause relatively benign illness in normal individuals but result in severe disease manifestations in patients with AIDS. These diseases include Pneumocystis carinii pneumonia, CNS toxoplasmosis, cryptosporidiosis, and isosporiasis. Pneumocystis carinii pneumonia (PCP) caused by Pneumocystis carinii, is the most common opportunistic infection in AIDS. It is seen in more than 80% of individuals with this syndrome. Although historically classified as a protozoan, this organism shares many biochemical characteristics with fungi. The onset of PCP may be insidious, and cough and dyspnea are the most common presenting symptoms. Auscultation of the lungs is often unremarkable, but diffuse infiltrates are commonly seen on chest radiographs. The diagnosis of PCP can be confirmed by identifying the organism on specimens obtained by sputum induction or bronchoalveolar lavage. Trimethaprim-sulfamethoxazole is the treatment of choice but is unfortunately associated with leukopenia and rash in many individuals. Both trimethaprim-sulfamethoxazole and aerosolized pentamidine are used prophylactically in patients at high risk for initial or relapsing infection. The appropriate use of these agents has resulted in improved survival for AIDS patients with PCP. Toxoplasmosis, due to Toxoplasma gondii, affects the central nervous system in patients with AIDS. Headache is a common presenting symptom, and both seizures and paresis can occur. A diagnosis of toxoplasmosis is strongly suspected in symptomatic individuals with ringed mass lesions noted on head CT. Patients with this condition are treated with a combination of sulfadiazine, pyrimethamine, and folinic acid. Cryptosporidiosis and isosporiasis are coccidian protozoan diseases that can result in severe, acute, and chronic diarrhea in immunocompromised individuals. Cryptosporidiosis is the more common of the two and is caused by an unknown species of the genus crytosporidium. Isosporiasis is due to infection with Isospora belli. Dehydration and weight loss are a common result of infection with either agent. A definitive diagnosis can be made by examining an acid fast stain of a diarrheal stool specimen and demonstrating oocysts that are specific for each of these organisms. Fluid replacement and general supportive care are essential in the treatment of both of these diseases. Spiramycin is an unproven treatment modality that is often used in patients with cryptosporidiosis. Isosporiasis responds to initial therapy with trimethaprim-sulfamethoxazole, followed by prophylaxis with pyrimethamine. The adoption of safe sexual practices that minimize fecal-oral contamination should decrease the future prevalence of these diseases and other enteric parasitic infections.