Trigeminal sensory nuclei are the first processing stage in the vibrissal system of rodents. They feature separate populations of thalamic projecting cells and a rich network of intersubnuclear connections, so that what is conveyed to the cortex by each of the ascending pathways of vibrissal information depends on local transactions that occur in the brainstem. In the present study, we examined the nature of these intersubnuclear connections by combining electrolytic lesions with electrophysiological recordings, retrograde labeling with in situ hybridization, and anterograde labeling with immunoelectron microscopy. Together, these different approaches provide conclusive evidence that the principal trigeminal nucleus receives inhibitory GABAergic projections from the caudal sector of the interpolaris subnucleus, and excitatory glutamatergic projections from the caudalis subnucleus. These results raise the possibility that, by controlling the activity of intersubnuclear projecting cells, brain regions that project to the spinal trigeminal nuclei may take an active part in selecting the type of vibrissal information that is conveyed through the lemniscal pathway.