Subepiglottic cysts are an uncommon cause of respiratory noise in young horses. They are likely present from birth but remain undetected until the horse begins exercise training. These cysts are suspected to arise from remnants of the thyroglossal duct. Clinical signs include respiratory noise and exercise intolerance. Large cysts may produce coughing, dysphagia, and aspiration in foals. Diagnosis is determined by endoscopic examination of the upper respiratory tract. The cyst appears as a smooth-walled, fluctuant mass that contains thick, yellow, mucoid material. Occasionally, the mass is not visible in the nasopharynx, and oral examination under general anesthesia may be required to identify it. Histologically, subepiglottic cysts are lined with a combination of stratified squamous and pseudostratified columnar epithelium. Treatment involves complete removal of the secretory lining of the cyst. Rupture of the cyst results in immediate decompression, but recurrence is common. The most common approach is ventral laryngotomy, although transendoscopic Nd:YAG laser surgery has been used for complete excision.