The epiglottis is the triangular flap that rests on the floor of the back of the throat and covers the windpipe (trachea) when a horse swallows. A sub-epiglottic cyst is a fluid-filled cyst (balloon) at the back of the throat, under the epiglottis. As the cyst grows, it can interfere with air flow, causing respiratory noise and in some cases, causing poor performance. It can also interfere with the function of the epiglottis in protecting the airway during swallowing. For this reason, some horses with this condition will cough when they are eating. Not all horses show clinical signs, especially when the cysts are small.
The origin of the cyst is thought to be developmental- present since birth but only noticed as the horse begins training. The cyst is usually filled with a mucoid substance.

This is an endoscopic diagnosis, although x-ray of the throat area has some diagnostic value.

Treatment is surgical removal. Surgery can be done in the standing horse with a surgical laser through an endoscope, or can be done under general anesthesia through an incision created through the larynx (laryngotomy)