Serotonin (5HT) binding sites in autonomic portions of the dorsomedial medulla oblongata of the rat were localized using autoradiographic techniques with radioactive ligands that express high affinity for the 5HT1 (3H-5HT), 5HT1A (3H-8OH-DPAT), or 5HT1B (125I-CYP with isoproterenol) receptor subtypes. 5HT1A sites were densely distributed in the nucleus tractus solitarius (NTS), with the highest densities localized to the interstitial subnucleus and the central subnucleus. 5HT1B sites were also found in the NTS, with the highest densities localized to the substantia gelatinosa subnucleus. The dorsal motor nucleus of the vagus nerve and nucleus ambiguus exhibited low densities of 5HT1B sites. However, the nucleus intercalatus, a cerebellar relay nucleus that also contains dendrites of vagal parasympathetic preganglionic neurons and receives autonomic forebrain afferent input, showed very dense 5HT1B sites. The promontorium, paratrigeminal islands, and the dorsomedial portion of the trigeminal nucleus (DM5), which are areas of viscerosomatic integration, exhibited high densities of both 5HT1A and 5HT1B sites. The area postrema contained low levels of both 5HT1A and 5HT1B sites. Visceral deafferentation via cervical vagotomy or nodose ganglionectomy caused a significant decrease in 5HT1A sites in the interstitial subnucleus of the NTS ipsilateral to the lesion. No changes were seen in 5HT1B sites. These studies suggest that 5HT1A and 5HT1B sites are involved in the processing of visceral sensory information in the NTS and associated areas. Based upon viscerotopic organization of the NTS, 5HT1A sites appear preferentially distributed in portions of the NTS that are associated with the coordination of swallowing, respiration, and cardiovascular function, while 5HT1B sites appear preferentially distributed in areas of the NTS associated with gastrointestinal, hepatic, pancreatic, and cardiovascular function. However, since these association were not absolute and there was a great deal of overlap between the two sites, speculation regarding their specific functions in autonomic control must await pharmacological examination.