We describe three patients with acquired immunodeficiency syndrome who presented with a bilateral coarse superficial epithelial keratitis due to infection with the protozoal parasite Microspora, Encephalitozoon cuniculi. Despite the extent of the corneal surface disease, conjunctival inflammation was minimal. Visual acuity ranged from 20/20 to 20/200. In one patient, the keratitis was complicated by the development of a surface defect with secondary Pseudomonas species infection. All patients had a history of exposure to household pets. Standard cultures were negative. Diagnosis was established in two of the three cases based on characteristic appearance of the protozoan in conjunctival scrapings. Electron microscopy of a conjunctival biopsy specimen in one patient confirmed the species. No recognized effective treatment is available for this infection.