The afferent projection pattern from individual vibrissae follicles was related to the distribution of cytochrome oxidase (CO) dark cell clusters in the trigeminal sensory nuclei of adult rats to determine whether segregated primary afferent projections limit the extent of the topographic reorganizations that can occur at the level of the brainstem on a short term basis after changes in sensory driven activity. The results indicate that the projections to all the brain stem trigeminal subnuclei, including the principal sensory nucleus and the three subdivisions of the spinal trigeminal nucleus, are topographic; however, the extent to which label from different whisker rows overlap appears to differ from subdivision to subdivision. In the principal sensory nucleus there is nearly a one to one relationship between the inputs from the vibrissae follicles and the corresponding CO-dense clusters. Thus, little overlap of inputs from different vibrissae rows is likely. In contrast, in the pars interpolaris and, to a lesser extent, in the pars caudalis, inputs from individual vibrissae follicles extend beyond the appropriate CO-dark patch into adjacent whisker patches; thus, inputs to these subdivisions from different vibrissae likely overlap more extensively.