The pharynx connects the oral cavity and the esophagus. It is the common passageway for food and air. The following structures open into the pharynx: the caudal nares, the mouth, two auditory tubes, the larynx, and the esophagus.

During inspiration, air enters the pharynx through the two caudal nares. From the pharynx, air on its way to the trachea, crosses the larynx. The auditory tubes (also called eustachian tubes) connect the middle ear and the pharynx. This connection helps to equalize air pressure on both sides of the ear drum, which separates the external air and the middle ear. During deglutition (swallowing), when the bolus of food is plunged into the pharynx by the tongue, the pharynx shortens and its muscle contractions force food into the esophagus. The muscles of the pharynx are voluntary striated muscles controlled by nerves from the brain. The swallowing center in the medulla of the brain coordinates swallowing in between respiratory movements. Once a bolus of food is in the esophagus, it is moved to the stomach by peristalsis.

Note that other parts of the muscles of the gut are smooth involuntary muscles controlled by the autonomic nervous system and the myenteric plexuses part of the gut nervous system, situated between the circular and longitudinal muscle layers.