Stromal keratitis and iritis developed in the left eye of a healthy 45-year-old man with no history of ocular disease, trauma, or contact lens wear. The clinical course over a 2-year period was characterized by progressive central disciform keratitis, recurrent anterior stromal patchy infiltration, and iritis which was partially controlled with topical corticosteroids and broad-spectrum antibiotics. Results of bacterial, viral, fungal, and chlamydial cultures were negative. Results of histopathologic examination of a corneal biopsy specimen and, later, a penetrating keratoplasty specimen showed many extracellular and intracellular spores in degenerating keratocytes. By electron microscopy there were encapsulated oval structures measuring approximately 3.5 to 4 microns in length x 1.5 microns in width. Mature spores had well-developed cell walls that contained two abutted nuclei (diplokaryon) and a redundant polar tubule with six coils. These structures are characteristic of a protozoa in the genus Nosema.