To understand better how the brainstem may influence thalamocortical activity, we have examined the projection patterns of different brainstem nuclei to the thalamic reticular nucleus. Iontophoretic injections of biotinylated dextran were made into various nuclei of the brainstem (superior colliculus, periaqueductal grey matter, parabrachial nucleus, pedunculopontine tegmental nucleus, laterodorsal tegmental nucleus, substantia nigra, ventral tegmental area, and locus coeruleus) of Sprague-Dawley rats by using stereotaxic coordinates. Our results show that afferents from each brainstem nucleus make distinct zones within the reticular nucleus. For example, the superior colliculus projects largely to the dorsal parts of the reticular nucleus, whereas the pedunculopontine nucleus projects to the ventral parts of the reticular nucleus. The substantia nigra, on the other hand, projects to the ventrolateral edge of the reticular nucleus. We also examined the distribution of these brainstem afferents within the dorsal thalamus and compared these distributions with those seen in the reticular nucleus. We found three different patterns. First, a given brainstem nucleus projects to a particular dorsal thalamic nucleus as well as to the corresponding, functionally associated, reticular sector (e.g., from the substantia nigra). Second, a given brainstem nucleus projects to a particular dorsal thalamic nucleus but not to the corresponding reticular sector (e.g., from the superior colliculus). Finally, a given brainstem nucleus projects to a given reticular sector but not to the corresponding dorsal thalamic nucleus (e.g., from the midbrain reticular nucleus). In general, our results indicate that various brainstem nuclei project to particular territories of the thalamic reticular nucleus. Through these reticular projections, brainstem nuclei may influence distinct thalamocortical pathways in addition to those that are influenced by their direct projection to the dorsal thalamus.