Congenital cysts, sinuses, or fistulae of the branchial arch apparatus or thyroglossal duct have been reported in horses, dogs, cats, and ruminants, yet are very rare. These structures arise from persistent embryologic pharyngeal pouches, arches, or clefts, or the thyroglossal duct. Animals typically present with nonpainful, fluid-filled masses in the cervical region. Clinical signs are typically due to the space-occupying mass and include dyspnea, respiratory stridor, intermittent esophageal obstruction, and coughing. Animals may present later in life; it is not known why a cyst may suddenly enlarge but may be associated with respiratory infection. Diagnostic imaging includes radiography, ultrasonography, video endoscopy, and contrast CT to determine whether there is communication with the pharynx. Branchial cysts (also called lateral cervical cysts) in horses are typically seen on the right side, although a bilateral case has been reported. Surgical excision is curative, although complications include right laryngeal hemiplegia, seroma formation, and pneumonia. Alternatively, some horses have been treated with marsupialization and iodine sclerotherapy with good results. In dogs and cats, few complications have been noted. Embryologic origin of branchial cysts has been mostly of the third pharyngeal pouch, although anatomic location has also suggested origin of the fourth and sixth pouches in some cases.