We describe an unusual case of proventriculitis associated with Cryptosporidium baileyi in a 7-wk-old snowy owl (Bubo scandiacus) chick kept at a zoo. Necropsy of this animal revealed diffuse mucosal thickening of the proventriculus. Subsequent histopathological examinations of the proventriculus showed marked ductal epithelial hyperplasia with intestinal metaplasia and severe inflammatory cell infiltration in the lamina propria and submucosa. These lesions were associated with numerous periodic-acid-Schiff-positive cryptosporidia-like protozoan parasites. Moreover, oocysts found within the lamina propria had a noticeably thicker wall and displayed Ziehl-Neelsen-positive test results. PCR sequencing analyses of the 18S rDNA, actin, and 70 kDa heat shock protein gene loci identified the protozoan to be C. baileyi, of which two novel sets of primers were designed for use with formalin-fixed paraffin-embedded tissue. An epidemiological survey was carried out at the zoo to investigate the source of infection, but all owl species surveyed proved negative for cryptosporidiosis. It is most likely that small animal vectors such as wild birds or rodents were responsible for this particular lethal case. This is the first report of C. baileyi associated with proventriculitis and also the first report of cryptosporidiosis in a raptor species in Asia.