Four falcons from a private collection of 137 falcons in Abu Dhabi (UAE) died suddenly in summer 2005. In order to screen for a possible disease among the remaining falcons in the aviary, all other birds were caught, examined and treated if necessary. Most of the falcons suffered from massive lice infestation and 74 falcons additionally from a heavy Caryospora sp. burden. Endoscopy revealed yellowish plaques on intestines, livers or kidneys in 70 birds (51.1% morbidity). Proliferative serositis was seen in 17 out of 24 necropsied birds with plaques on intestines, livers or kidneys, which did not resemble any known disease in falcons. However, apart from 20 falcons, which died within a 6-week period after the initial examinations due to advanced disease stages, all other falcons responded well to the treatment with dimetridazole (Emtryl), indicating protozoal disease. Immunohistochemistry confirmed the presence of microsporidial antigen. The final diagnosis of Enterocytozoon (E.) bieneusi genotype D was confirmed with materials from 6 birds by PCR and sequencing. To our knowledge this is the first report of microsporidiosis caused by E. bieneusi in raptors in general and in falcons in particular. However, it is still unclear for how long E. bieneusi was present in the falcon flock, and which role it played in the development of the disease. Predisposing factors such as high temperature and overcrowding in the aviary induced immune suppression causing massive lice infestation as well as coccidiosis, thus paving the way for invasion with microsporidial spores.