Following injections of [3H]leucine into the formatio reticularis gigantocellularis (Rgc), reticularis pontis caudalis (Rpc), reticularis pontis oralis (Rpo), reticularis mesencephali (Rmes), or the locus coeruleus (LC) of the rat, autoradiographic study revealed prominent reticuloreticular projections from all areas and secondary projections onto cranial nerve motor nuclei from most areas within the brain stem. Common long descending projections extended the full length of the spinal cord terminating in the ventromedial ventral horn and intermediate zone and more sparsely in the base of the dorsal horn and (particularly from Rgc) the region of the motoneurons. Common long ascending projections extended into the forebrain via Forel's tegmental fascicles. A dorsal branch of fibers innervated the intralaminar and midline nuclei of the thalamus. The major fiber system continued forward through Forel's fields and ascended into the pallidum from Rpo, Rmes, and LC and into the neostriatum from Rmes and LC. Fascicles from all areas also ascended in the medial forebrain bundle through the lateral hypothalamus to the lateral preoptic area, substantia innominata, and nuclei of the diagonal band. From Rpo, Rmes, and LC, fibers continued forward to reach the cerebral cortex, where the innervation was sparse and discrete from Rpo and Rmes but moderate and ubiquitous from LC. Retrograde transport of true blue and/or nuclear yellow revealed inverse gradients along the brain stem longitudinal axis of interdigitated cells respectively projecting caudally into the spinal cord (with the greatest number of cells in Rgc, Rpc, and Rpo) and rostrally into the diencephalon (with the greatest number of cells in Rmes and LC), with very few cells projecting both to the spinal cord and the diencephalon. From the basal forebrain, a large number of reticular and LC cells were retrogradely labelled, whereas from the frontal cortex, a much smaller number of reticular cells was labelled. These results document the widespread efferent projections from the reticular formation and overlapping, yet more extensive, projections from the LC.