This study analysed the organization of central nervous system networks involved in the processing of meningeal inputs in the male, Sprague-Dawley rat. We injected the anterograde tracer, biotin dextran, into areas of the medullary trigeminal nucleus caudalis (Sp5C), which receive inputs from the ophthalmic division of the trigeminal nerve. Double-labelling immunohistochemical studies were then performed to compare calcitonin gene-related peptide (CGRP) or serotonin 1D (5HT1(D)) receptor distributions in the areas innervated by Sp5C neurons. Dense, topographically organized intratrigeminal connections were observed. Sp5C neurons projected to the commissural subnucleus of the solitary tract, A5 cell group region/superior salivatory nucleus, lateral periaqueductal grey matter, inferior colliculus and parabrachial nuclei. Trigeminothalamic afferents were restricted to the posterior group and ventroposteromedial thalamic nuclei. Some of these areas are also immunoreactive for 5HT1(D) and CGRP and thus remain potential central targets of triptan molecules and other antimigraine drugs.