The catecholamine (CA) innervation of the rat brainstem was studied by biochemical analysis of discrete nuclei or areas and by glyoxylic acid-formaldehyde freeze dry fluorescence histochemistry. CA assays demonstrate that the highest norepinephrine (NE) content in brainstem is present in the trigeminal motor nucleus, nucleus tractus solitarius, dorsal motor nucleus of the vagus and nucleus raphe dorsalis. Bilateral locus coeruleus (LC) lesions do not significantly alter NE content in these nuclei but do decrease NE content in the superior and inferior colliculi, medial geniculate body, interpeduncular nucleus, pontine nuclei and the main sensory trigeminal nucleus (60-75%). Dopamine (DA) and epinephrine (E) are found in significant concentration in only a few of the nuclei examined. Fluorescence histochemical analysis indicates that two groups of NE axons innervate rat brainstem. LC neuron axons with a distinctive morphology principally innervate sensory and association nuclei of the brainstem. These disappear completely after bilateral LC lesions. The second group of axons originates from lateral and dorsal tegmental NE cell groups. Primary motor and visceral nuclei are densely innervated by fine and thick axons from these groups. Lesions of LC do not alter the NE innervation in any of the nuclei which contain axons of the second group. These results indicate that the brainstem NE innervation is divided into two major systems. The locus coeruleus complex innervates mainly primary sensory and association nuclei whereas the lateral tegmental NE neurons innervate primary motor and visceral nuclei. Although some overlap is present, the LC and lateral tegmental NE systems predominantly innervate separate and functionally distinct areas of the brainstem. DA and E neurons provide a very minor component of the brainstem CA innervation.