This study explores for the first time the shape, volume, and configuration of nasal cavity structures of the endangered Patagonian huemul deer via computed tomography (CT). Three-dimensional (3D) reconstructions derived from data sets obtained from five Patagonian huemul deer skulls were analyzed. Using semiautomatic segmentation, 3D models were created of all the sinus compartments and nasal conchae. Volumetric measurements were taken of seven sinus compartments. The Patagonian huemul deer has a wide, large nasal cavity, with an osseous nasal aperture typical of cervids and a choana with characteristics that differentiate it from the pudu and roe deer. It also has six nasal meatuses and three nasal conchae, with the ventral nasal concha having the greatest volume and surface, which given its extension ensures a greater ability to humidify and heat the air. Further analysis showed the complex system of paranasal sinuses to be characterized by a rostroventral and interconnected group, where communication with the nasal cavity is common through the nasomaxillary opening, and a caudodorsal group that communicates with the nasal cavity through openings in the nasal meatuses. Our study of the endangered Patagonian huemul deer documents an intricate, and in some nasal cavity structures, unique morphological construction which may predispose it to higher rates of sinonasal afflictions due largely to its nasal complex anatomy, thus affecting its high cultural value.