The nucleus ambiguus has been reported to innervate various thoracic and abdominal viscera in addition to the musculature of the upper alimentary tract. However, the literature is contradictory as to how different regions of the nucleus ambiguus innervate specific organs. Therefore, a systematic investigation of the viscerotopic organization of the nucleus ambiguus was undertaken. In 102 rats, 0.5-10.0 microliter of HRP, WGA-HRP, cholera toxin-HRP or fluorescent tracers were injected into the IXth, Xth, and XIth cranial nerves and the major branches of the Xth as well as organs supplied by them. The results demonstrate that the nucleus ambiguus in the rat is made up of two major longitudinal divisions: a dorsal division comprised of three rostrocaudally aligned subdivisions representing the special visceral efferent component, and a ventral division comprised of at least two subdivisions representing the general visceral efferent component. The dorsal division corresponds to the nucleus ambiguus in the narrow sense and comprises a rostral esophagomotor compact formation, an intermediate pharyngolaryngomotor semicompact formation, and a caudal laryngomotor loose formation. Each of these formations displays a characteristic dendroarchitecture. The stylopharyngeal and cricothyroid motoneurons are displaced rostrad from the main pharyngeal and laryngeal motoneuronal pools. Thyropharyngeal (lower constrictor) motoneurons occupy the rostral half of the semi-compact formation and hyopharyngeal (middle constrictor) motoneurons its entire length. The ventral division of the nucleus ambiguus corresponds to the external formation, extends along the entire length of the medulla oblongata, and contains preganglionic neurons innervating the heart and supradiaphragmatic structures innervated by the glossopharyngeal and the superior laryngeal nerves.