The guttural pouches are paired outpocketings of the upper airway (pharynx). They are located near the throatlatch region of the neck. Major vessels and nerves supplying the head course through the walls of the pouch. The pouch is accessed with an endoscope through a small slit in the pharynx.

The guttural pouches are thought to be involved in cooling blood that passes to the brain through the large carotid arteries. They may also have a role in equalizing air pressure on the tympanic membrane. The guttural pouch volume in an average horse is 300-500 ml each.

An empyema is a collection of pus in a natural body cavity, in this case the guttural pouch. Infection can become established in the guttural pouches as an extension from upper airway bacterial infection, and tends to persist because of the anatomy of the pouch. Guttural pouch empyema produces pus discharge from one nostril or both.

Chondroids are firm "stones" of pus that form here and complicate treatment of infection. In milder cases, guttural pouch infections respond to systemic antibiotics or flushing of the pouch. More difficult cases, and those with chondroids often require surgery.