Histochemistry for cytochrome oxidase reveals a vibrissa-related pattern in trigeminal nucleus principalis, subnucleus interpolaris, and the magnocellular portion of subnucleus caudalis. This pattern is apparent in late fetal animals and is disrupted by transection of the infraorbital nerve on the day of birth. We recently reported results suggesting that the cytochrome oxidase pattern reflects primary afferent-induced clustering of second order neurons in all of these nuclei. If this conclusion is correct, it should follow that primary afferent lesions made after the cytochrome oxidase pattern became established in the brainstem might have little effect upon it. Accordingly, we transected the infraorbital nerve (the trigeminal branch that supplies the vibrissae) on postnatal days 0-10 and evaluated the vibrissa-related pattern in the brainstem with cytochrome oxidase histochemistry at varying intervals after these lesions. If the infraorbital nerve was sectioned on postnatal days 0-2, the vibrissa-related pattern was absent in trigeminal nucleus principalis, and both subnucleus interpolaris and caudalis. If such lesions were made after postnatal day 9, there was no appreciable effect upon the cytochrome oxidase pattern in any portion of the trigeminal brainstem complex. However, if lesions were made between postnatal days 3 and 8, the density and clarity of the cytochrome oxidase staining pattern were reduced in interpolaris and caudalis, but not in principalis. This difference was not due to differential transganglionic degeneration in these nuclei. Tracing with horseradish peroxidase demonstrated qualitatively equivalent primary afferent losses in principalis, interpolaris, and caudalis. Immunocytochemistry with a monoclonal antibody directed against parvalbumin also demonstrated a vibrissa-related pattern of cell bodies in principalis and interpolaris in rats killed on postnatal day 9 or later ages. The combination of retrograde tracing and immunocytochemistry revealed that the parvalbumin-immunoreactive neurons in principalis projected to thalamus while those in interpolaris were not labelled by tracer injections into the thalamus, midbrain, cerebellum or spinal cord. Infraorbital nerve transections made as late as postnatal day 8 resulted in a sharp decrease in the staining of parvalbumin-positive neurons in interpolaris, but not in principalis. Lesions made on postnatal day 10 had no qualitative effect upon parvalbumin-positive neurons in any portion of the trigeminal brainstem complex. The results of this study support the conclusion that the vibrissa-related cytochrome oxidase pattern in principalis becomes independent of primary afferent input at a very short interval after its initial appearance. In contrast, the patterns in more caudal portions of the trigeminal brainstem complex require maintenance of primary afferent input for a much longer postnatal period.(ABSTRACT TRUNCATED AT 400 WORDS)