Cryptosporidiosis has been reported in more than 30 avian species worldwide. Although some cases of cryptosporidiosis have been described in captive birds of prey in the order Falconiformes, to date there have been no reports of the disease in wild raptors. Here we describe for first time an ocular and respiratory disease associated with Cryptosporidium baileyi in wild scops owl (Otus scops, order: Strigiformes). Sixteen otus owl fledglings born in the wild during the summer of 2008 were admitted to the Torreferrussa Wildlife Rehabilitation Centre (Catalonia, northern Spain) in July and August of the same year. In the middle of September, blepharoedema, conjunctival hyperaemia and mucopurulent ocular discharge were diagnosed unilaterally in 75% (12/16) of the birds and bilaterally in 25% (4/16). Moreover, five birds (31%) developed diffuse epithelial corneal oedema, one owl (6%) displayed mild anterior exudative uveitis and another developed rhinitis (6%). Two birds were euthanized because of the severity of disease. The histopathology demonstrated cryptosporidia-like structures in the conjunctival cells and in the nasal respiratory epithelium of one owl. Cryptosporidium spp. oocysts (6.5 to 7.0 x 5.0 to 5.5 microm) were identified by immunofluorescent antibody test (IFAT) in histological sections from eyelids, trachea and respiratory sinuses and in swab samples from the glottis, choanal slit and conjunctival sac. Polymerase chain reaction and DNA sequence analysis confirmed the presence of C. baileyi. Birds were treated orally with azithromycin (40 mg/kg) once a day for 15 days, and by the end of the treatment all owls tested negative for the parasites, by IFAT, and did not display further signs of disease.