GAP-43 (B-50,F1,pp46) is a neuron-specific phosphoprotein that has been implicated in the development and modulation of synaptic relationships. Although most neurons cease expressing high levels of GAP-43 after the completion of synaptogenesis (Jacobson et al., 1986), certain brain regions continue to have considerable amounts of the protein throughout life (Oestreicher et al., 1986); in at least one such area, the phosphorylation of the protein has been linked with the events that underlie synaptic potentiation (Lovinger et al., 1985). In this study, we used the indirect immunoperoxidase method to map the distribution of GAP-43/B-50 in the brains of 8 adult rats with 2 different antibodies: a monospecific, polyclonal antibody prepared in sheep against the purified protein and an affinity-purified IgG prepared in rabbits. Specific immunoreactivity was found primarily in the neuropil and followed a generally increasing caudal-to-rostral gradient along the neuraxis. Densest staining occurred in layer I of the cortex, the CA1 field of the hippocampus, and in a continuum of subcortical structures that included the caudate-putamen, olfactory tubercle, nucleus accumbens, bed nucleus of the stria terminalis, amygdala, and medial preoptic area-hypothalamus. In the brain stem, staining was seen in the central gray and in ascending visceral relay nuclei, but was essentially absent in areas related to ascending somatosensory information (e.g., the cochlear nuclei or vestibular complex) and motor control (e.g., nucleus ruber or the motor nuclei of the cranial nerves). Staining in dorsal thalamus was likewise modest in most somatosensory and somatomotor relay nuclei, but dark in certain other structures (e.g., mediodorsal nucleus, lateral complex). This distributional pattern raises the question of whether synapses in all areas containing high levels of GAP-43/B-50 are capable of undergoing functional plasticity, or whether the protein may function in some of these areas in some other capacity (e.g., general signal transduction).