A 20-month-old, intact male shih tzu was evaluated for chronic upper airway disease. Endoscopic examination established a diagnosis of choanal atresia, a developmental anomaly of the posterior nasal cavity. Although surgical intervention provided temporary relief, stenosis of the nasopharynx by obstructive scar tissue was confirmed within four weeks. A permanent tracheostomy provided long-term relief of the respiratory difficulty. This is the first report of choanal atresia or nasopharyngeal stenosis in a dog.