A 7-week-old male Saker falcon died with a history of severe refractory dyspnoea and respiratory signs. Microscopical lesions included moderate to severe lymphoplasmacytic inflammation of the middle ears, conjunctivae, third eyelids, choanae, salivary glands of the tongue, turbinates, larynx, trachea, syrinx and bronchi. The lesions were associated with variable numbers of Cryptosporidium spp., further confirmed by transmission electron microscopy and in-situ hybridization. Cryptosporidium baileyi was identified by DNA sequence analysis. C. baileyi may therefore be a cause of otitis media in raptors as it is in man. It is most likely that the middle ears of the Saker falcon acquired the infection through the eustachian tubes that originate near the pharynx in the oral cavity. This is the first description of otitis media associated with C. baileyi in a bird or a mammal except man[...]