CASE DESCRIPTION A 4-hour-old 6.3-kg (13.9-lb) female alpaca cria was evaluated because of severe respiratory distress and difficulty nursing since birth. CLINICAL FINDINGS The cria had open-mouth breathing and cyanotic membranes, with no airflow evident from either nostril. Supplemental oxygen was delivered, and the patient was anesthetized and intubated orotracheally; a CT evaluation of the head confirmed bilateral membranous obstruction of the nasal cavities, consistent with complete bilateral choanal atresia. TREATMENT AND OUTCOME Choanal atresia was treated with an endoscopically assisted balloon-dilation technique, and temporary tracheostomy was performed. Stenosis recurred, requiring revision of the repair and intranasal stent placement 3 days after the first surgery. The tracheostomy tube was removed the next day. Complications during hospitalization included mucoid obstruction of the tracheostomy tube, granulation tissue development in the trachea near the tracheostomy site, mucoid stent obstruction, aspiration pneumonia, and presumed partial failure of passive transfer of immunity. The stents were removed 2 weeks after admission, and the cria was discharged 3 days later. The owner was advised that the animal should not be bred. At last follow-up 3 years later, the alpaca was doing well. CLINICAL RELEVANCE Surgical treatment with a balloon-dilation technique and placement of nasal stents with endoscopic guidance were curative in this neonatal alpaca with bilateral membranous choanal atresia. Computed tomography was useful to determine the nature of the atresia and aid surgical planning. Because a genetic component is likely, owners should be advised to prevent affected animals from breeding.