Airway obstruction is a common cause of poor performance in horses. Structural abnormalities (insufficient length, rigidity) can be a cause for the obstruction. Currently, there are a few effective clinical options for reconstruction of the equine larynx. A regenerative medicine approach to reconstruction may provide the capability to stabilize laryngeal structures and to encourage restoration of site-appropriate, functional, and host-derived tissue. The purpose of this study was the histopathological evaluation of (1) decellularization of equine (horse) laryngeal cartilages (epiglottis and arytenoids); (2) the host response to decellularized laryngeal cartilages implanted subcutaneously in a donkey model as a test of biocompatibility; and (3) the use of decellularized laryngeal cartilages in a clinically relevant pilot study in the horse larynx. Equine laryngeal cartilages were found to be sufficiently decellularized and were subsequently implanted subcutaneously in donkeys to test biocompatibility. After 4 weeks, the implanted cartilage was harvested. In the subcutaneous model, the samples did not elicit a rejection or foreign body type reaction and were judged suitable for implantation in a clinically relevant equine model. Implants were placed in the upper airway (arytenoids and epiglottis) of one horse. At 4 weeks, the implants were observed to remodel rapidly and were replaced by dense connective tissue with signs of new hyaline cartilage formation in the arytenoids and by connective tissue containing glandular structures and an epithelial covering in the epiglottis. The results of the present study demonstrate the feasibility of a scaffold-based regenerative medicine approach to reconstruction of the equine upper airway; however, further studies investigating long-term integration, formation of new cartilage, and mechanical properties are needed.