A total of 123 avian faecal specimens randomly collected in Bohemian commercial aviaries, Zoo parks and countryside were screened for the presence of human pathogenic microsporidia by both calcofluor M2R staining and polymerase chain reaction. Of these, no positive sample was detected using microscopical examination, and one isolate was detected by polymerase chain reaction and identified as Encephalitozoon cuniculi. Cockateel (Nymphicus hollandicus) represents a new avian host of this microsporidian.