Serotonin (5HT) binding sites in the medulla oblongata of the rat were localized using autoradiographic techniques with radioactive ligands that express high affinity for the 5HT1 (3H-5HT), 5HT1A (3H-80H-DPAT), or 5HT1B (125I-CYP with isoproterenol) receptor subtypes. 5HT1A sites were concentrated primarily in certain sensory regions of the medulla and in regions that contain serotonergic neurons. 5HT1B sites were diffusely distributed throughout the reticular formation and motor regions as well as being localized to certain sensory regions. A surprising finding was an association of 5HT1B binding sites with the corticospinal tract. 3H-5HT binding generally reflected the combined pattern of 5HT1A and 5HT1B sites but was also extremely dense in the choroid plexus, which exhibited virtually no 5HT1A or 5HT1B ligand binding. Presumably this binding, which was blocked by ketanserin, corresponds to 5HT1C sites. Administration of the serotonergic neurotoxin 5,7-dihydroxytryptamine reduced 5HT1A binding sites in regions of the medulla that contain serotonergic neuronal cell bodies. 5HT1B binding was not significantly altered in any area of the medulla. These studies indicate an important role for 5HT1A ligands in the processing of visceral and somatic sensory information, in regulation of certain cerebellar afferent projections, and in the regulation of serotonergic neuronal activity. 5HT1B ligands would be expected to regulate visceral and somatic efferent activity, as well as sensory information and reticular efferent activity, and might presynaptically regulate cortical inputs to the brain stem and spinal cord.