Acquired immunodeficiency syndrome (AIDS) cholangiopathy is a clinical syndrome characterized by right upper quadrant pain, low-grade fever, and bile duct dilatation or papillary stenosis. Cryptosporidia and cytomegalovirus have been most commonly reported as causes of AIDS cholangiopathy, but recently microsporidia have also been recognized as a causative agent. We here report an additional case of AIDS cholangiopathy with the microsporidian Encephalitozoon (Septata) intestinalis. Because this microsporidial species can disseminate throughout the body and is susceptible to treatment by albendazole, it is important to identify and separate this organism form other causes of AIDS cholangiopathy. A key histologic feature seen in this case, which has not been observed in AIDS cholangiopathy caused by other parasitic organisms, is the presence of numerous foamy macrophages in the lamina propria, which contain the microsporidial organisms, as seen by electron microscopy. The presence of these foamy macrophages may be an important histologic clue to the presence of infection by Encephalitozoon intestinalis.