Extrapulmonary infection with Pneumocystis carinii in AIDS patients on aerosolized pentamidine is occurring more frequently. We report five patients diagnosed with gastrointestinal pneumocystosis while on aerosolized pentamidine prophylaxis and have identified infections involving the peritoneum, liver, and transverse colon, as well as stomach and duodenum. Physicians should have a high index of suspicion for extrapulmonary pneumocystosis, especially involving the gastrointestinal system, in HIV-infected patients, and early diagnosis must he pursued aggressively. The use of aerosolized pentamidine as prophylaxis for P. carinii pneumonia is not protective against gastrointestinal pneumocystosis because of inadequate systemic distribution of the drug. To our knowledge, this is the first report in a clinical journal documenting and photographing P. carinii organisms in ascitic fluid.