Corneal afferent nerves project to two spatially distinct sites within the spinal trigeminal nucleus: the subnucleus interpolaris/caudalis transition and the subnucleus caudalis/upper cervical spinal cord transition. The role of these two regions in processing corneal input is uncertain. To determine if neurons in these regions encode different features of an applied corneal stimulus, immunoreactivity for the immediate early gene protein product, Fos, was quantified in barbiturate-anesthetized rats. Intensity was varied across thermal (thermal probe 5, 35, 42, 52 degrees C; radiant heat of approximately 45 degrees C) stimuli and compared with that seen after mustard oil (5 microliters, 20%) or mineral oil application. All stimuli increased the number of Fos-positive neurons located at the ventrolateral pole of the subnucleus interpolaris/caudalis transition compared with unstimulated controls. By contrast, only 52 degrees C thermal probe and mustard oil produced an additional peak of Fos-positive neurons within the superficial laminae at the subnucleus caudalis/cervical cord transition. Further, the magnitudes of the bimodal peaks of Fos produced by 52 degrees C thermal probe and mustard oil stimuli were different quantitatively. Mustard oil caused a greater Fos response at the subnucleus interpolaris/caudalis transition than 52 degrees C thermal probe stimulation, whereas the opposite was true at the subnucleus caudalis/cervical cord transition. Double-labeling revealed that Fos immunoreactive neurons within the spinal trigeminal nucleus were restricted to regions densely labeled for calcitonin gene-related peptide. These results indicate that select features of corneal stimuli such as modality are encoded differently by neurons in the trigeminal subnucleus interpolaris/caudalis transition compared with those located in the subnucleus caudalis/cervical cord transition. It is likely that neurons in these two brainstem regions subserve different aspects of corneal sensation.