The phases of swallowing are controlled by central pattern-generating circuitry of the brain stem and peripheral reflexes. The oral, pharyngeal, and esophageal phases of swallowing are independent of each other. Although central pattern generators of the brain stem control the timing of these phases, the peripheral manifestation of these phases depends on sensory feedback through reflexes of the pharynx and esophagus. The dependence of the esophageal phase of swallowing on peripheral feedback explains its absence during failed swallows. Reflexes that initiate the pharyngeal phase of swallowing also inhibit the esophageal phase which ensures the appropriate timing of its occurrence to provide efficient bolus transport and which prevents the occurrence of multiple esophageal peristaltic events. These inhibitory reflexes are probably partly responsible for deglutitive inhibition. Three separate sets of brain stem nuclei mediate the oral, pharyngeal, and esophageal phases of swallowing. The trigeminal nucleus and reticular formation probably contain the oral phase pattern-generating neural circuitry. The nucleus tractus solitarius (NTS) probably contains the second-order sensory neurons as well as the pattern-generating circuitry of both the pharyngeal and esophageal phases of swallowing, whereas the nucleus ambiguus and dorsal motor nucleus contain the motor neurons of the pharyngeal and esophageal phases of swallowing. The ventromedial nucleus of the NTS may govern the coupling of the pharyngeal phase to the esophageal phase of swallowing.