The localization of MARCKS (myristoylated, alanine-rich C-kinase substrate), a major specific substrate for protein kinase C, has been studied in the rat brain. Light microscopic immunocytochemistry and biochemical analysis demonstrated that the protein is widespread throughout the brain and enriched in certain regions, including the piriform and entorhinal cortices, portions of the amygdaloid complex, the intralaminar thalamic nuclei, the hypothalamus, the nucleus of the solitary tract, nucleus ambiguus, and many catecholaminergic and serotonergic nuclei. Electron microscopic analysis revealed immunoreactivity in axons, axon terminals, small dendritic branches, and occasionally in dendritic spines. In neuronal processes, immunoreactivity was particularly prominent in association with microtubules, but reaction product was also seen in cytosol and adjacent to plasma membranes. No reaction product was observed in large dendrites, somata, or nuclei. A population of strongly immunoreactive glial cells was also observed. Many of these glial cells were morphologically similar to microglial cells, although some resembled astrocytes. In glial cells, both cytoplasm and plasma membranes were heavily labeled. The distribution of the MARCKS protein did not coincide precisely with the distribution of any of the subspecies of protein kinase C. The results indicate that the MARCKS protein is expressed in the majority of cell types in the CNS, and they suggest that the protein may be involved both in glial cell functions and in neuronal functions involving cytoskeletal elements in small dendritic branches and axon terminals.