A 3-week-old Friesian colt with a history of respiratory distress since birth was presented to our facility. Results after an endoscopy showed obstruction of the right nasal passage to the nasopharynx. Computed tomography was performed to further characterize this unilateral blockage. The images demonstrated a complete membranous obstruction of the ventral meatus, along with deviation of the vomer bone toward the left side of the nasal cavity. The diagnosis of unilateral choanal atresia was confirmed. This report is the first to describe computed tomographic features of choanal atresia in a foal.