The presence of neuropeptides in brainstem neurons that project to the medial and lateral thalamus and zona incerta has been studied in the rat. Brainstem neurons were retrogradely labeled from the medial and lateral thalamus and the zona incerta by colloidal gold-WGA-HRP and, after silver intensification of the retrograde label, their content of immunoreactivity for nine different neuropeptides was determined after colchicine administration. The medial thalamus and zona incerta both received a large peptidergic input and the lateral thalamus a smaller input from neurons in several brainstem nuclei. These were principally from the locus coeruleus, parabrachial nucleus, the dorsal raphe and the dorsal tegmentum. The principal input to the medial thalamus arose from neurotensin, neuropeptide Y and galanin neurons in the locus coeruleus, neurotensin neurons in the dorsal tegmentum, dynorphin neurons in the parabrachial nucleus and dorsal tegmentum, galanin neurons in the dorsal raphe, substance P neurons in the lateral and dorsal periaqueductal grey and calcitonin gene-related peptide neurons in the nucleus paragigantocellularis. The principal peptidergic input to the zona incerta was from dynorphin neurons in the nucleus of the solitary tract, bombesin neurons in the lateral reticular nucleus, calcitonin gene-related peptide and cholecystokinin neurons in the dorsal tegmentum, substance P, bombesin and galanin neurons in the locus coeruleus, dynorphin and substance P neurons in the lateral periaqueductal grey and cholecystokinin neurons in the substantia nigra, ventral tegmental nucleus and raphe linearis. The principal peptidergic input to the lateral thalamus came from calcitonin gene-related peptide and cholecystokinin neurons in the dorsal tegmentum, calcitonin gene-related peptide and galanin neurons in the locus coeruleus; substance P, neuropeptide Y, galanin and calcitonin gene-related peptide neurons in the dorsal raphe, substance P neurons in the lateral periaqueductal gray, galanin neurons in the nucleus interpedunculus and cholecystokinin neurons in the raphe linearis. In all these cases, from 25% to virtually all of the projection neurons in the brainstem nucleus could contain immunoreactivity to the neuropeptide. A lesser, but significant peptidergic input to the thalamus and zona incerta also arose from the trigeminal nucleus, the substantia nigra, the nucleus of the solitary tract, the lateral reticular nucleus, the interpeduncular nucleus, the raphe linearis, the paragigantocellularis, the inferior olive and ventral tegmental area. Overall, the neuropeptides most frequently present in the projection neurons were substance P, calcitonin gene-related peptide, galanin and cholecystokinin. Bombesin, neuropeptide Y, neurotensin and dynorphin were less common; and enkephalin was present in only a small percentage of projection neurons. Neurons in many of these brainstem nuclei receive nociceptive input from the spinal cord and then relay to the thalamus and zona incerta. Thus the neuropeptides we describe in these brainstem relay neurons could act to modulate the responses of thalamic neurons to their direct input from the spinothalamic tract.