Neurohistochemical methods using the retrograde and transganglionic transport of horseradish peroxidase (HRP) have been used to examine differences in the topographic representation in the brainstem of airway stretch receptors in the extrathoracic trachea and intrathoracic trachea of the cat. HRP neurohistochemistry has also been used to trace connections between brainstem respiratory nuclei, e.g., the inspiratory region of the nucleus of the tractus solitarius (nTS). Microiontophoretic deposits of HRP in functionally homogeneous neuronal populations of the medulla, the inspiratory neuronal group of the ventrolateral nTS, permit the examination of specific anatomical projections; distinct differences between the subnuclei of the nTS receiving projections from the extrathoracic and intrathoracic trachea could be identified. The afferents from the extrathoracic trachea (trachealis muscle stretch receptors) terminate in the main inspiratory subnucleus of the nTS, the ventrolateral nTS, whereas an identical region of the intrathoracic trachea sends its afferents to the dorsolateral nTS. The possible functional effects of such topographic differences are discussed. The inspiratory neuronal population in the ventrolateral nTS receives afferent projections from the contralateral rostral ventrolateral medulla. These afferent projections originate in a recently identified location in the rostral end of the nucleus ambiguous lying ventral to the retrofacial nucleus. This region has been identified as a site for respiratory related activity, which is expiratory in nature and anatomically distinct from the nucleus ambiguus and the retrofacial nucleus. This region has been identified as the Bötzinger complex, which corresponds to a collection of expiratory neurons in the rostral medulla.