Tachykinins (substance P, neurokinin A and neurokinin B) influence autonomic functions by modulating neuron activity in nucleus tractus solitarius (NTS) and dorsal motor nucleus of the vagus (DMV) through activation of neurokinin receptors NK1 and NK3. Our purpose was to identify and define by neurochemical markers, the subpopulations of NK1 and NK3 expressing neurons in NTS and DMV of rat and mouse. Because the distribution of the NK1 and NK3 expressing neurons overlaps, co-expression for both receptors was tested. By double labeling, we show that NK1 and NK3 were not co-expressed in NTS neurons. In the DMV, most of neurons (87%) were immunoreactive for only one of the receptors and 34% of NK1 neurons, 7% of NK3 neurons and 12% of NK1-NK3 neurons were cholinergic neurons. None of the neurons immunoreactive for NK1 or NK3 were positive for tyrosine hydroxylase, suggesting that catecholaminergic cells of the NTS (A2 and C2 groups) did not express neurokinin receptors. The presence of NK1 and NK3 was examined in GABAergic interneurons of the NTS and DMV by using GAD65-EGFP transgenic mouse. Immunoreactivity for NK1 or NK3 was found in a subpopulation of GAD65-EGFP cells. A majority (60%) of NK3 cells, but only 11% of the NK1 cells, were GAD65-EGFP cells. In conclusion, tachykinins, through differential expression of neurokinin receptors, may influence the central regulation of vital functions by acting on separate neuron subpopulations in NTS and DMV. Of particular interest, tachykinins may be involved in inhibitory mechanisms by acting directly on local GABAergic interneurons. Our results support a larger contribution of NK3 compared with NK1 in mediating inhibition in NTS and DMV.