An umbrella cockatoo (Cacatua alba) was presented with a keratoconjunctivitis of 9 months’ duration that was refractory to antibacterial and antifungal treatments. Microsporidian-type spores were observed in calcofluor M2R-stained cytological preparations of debrided corneal epithelium. Hematoxylin and eosin-stained sections of a conjunctival biopsy also showed a small number of intracellular parasites. Microsporidial DNA was detected by polymerase chain reaction in DNA extracted from the remaining biopsy material. Sequence analysis of the small subunit ribosomal RNA gene identified the microsporidium as Encephalitozoon hellem. The cockatoo was treated with oral albendazole for 3 months with resolution of the signs, and then again for 4 months when the signs returned. Since then, the bird has remained healthy for 2 years. This is the second report of a microsporidial keratoconjunctivitis in a bird, and the first report of an E. hellem infection in a cockatoo. Ophthalmologists should consider E. hellem as a possible cause of a keratoconjunctivitis in parrots that is refractory to treatment with traditional antimicrobials.