Retrograde and anterograde axonal transport techniques were used to investigate the organization of inputs from the dorsomedial medulla, a region known to elicit patterned swallowing reflexes following focal stimulation, to the fifth (MoV), seventh (VII), tenth (nucleus ambiguus, NA), and twelfth (XII) cranial nerve motor nuclei in the rat, those motor nuclei most directly involved in the control of deglutition. The results may be summarized as follows. 1) Dorsal medullary inputs to MoV, VII, and XII arise primarily from an extended region of the caudal reticular formation immediately ventral to the nucleus of the solitary tract (NTS), which we term the dorsal medullary reticular column (DMRC). Projections from the DMRC are largely bilateral and are distributed preferentially to the ventral subdivision of MoV, to the dorsal and intermediate subdivisions of VII, and to both the dorsal and the ventral subdivisions of XII. In addition, a subpopulation of large multipolar neurons embedded within the DMRC gives rise to a primarily crossed input to the dorsal subdivision of MoV. 2) Dorsal medullary inputs to the NA arise from the NTS, are largely uncrossed, and are organized such that the ventrolateral, intermediate, and interstitial subdivisions of the NTS project to the semicompact formation and to the rostral extension of the compact formation (which supplies the pharynx) and to the loose formation (larynx), whereas the central subdivision of the NTS provides input to the compact formation (esophagus). 3) Neither the NTS nor the DMRC gives rise to significant projections to the central subnucleus of the NTS. Together, these results provide evidence for discrete medullary pathways subserving sequential activation of swallowing reflexes. J. Comp. Neurol. 417:448–466, 2000. © 2000 Wiley-Liss, Inc.