Mitochondria contain hundreds of proteins, most of which are encoded by the nucleus. In neurons, distal dendrites and axon terminals can be separated from the nucleus by a great distance, and the mechanism by which precursor proteins reach distal neuronal processes is not well understood. While our previous study on cytochrome oxidase suggests a post-translational mechanism of delivery, it is not known whether precursor proteins reach their target processes before or after incorporation into mitochondria. In order to localize only precursor proteins and not the mature form of the subunit in neurons, we generated polyclonal antibodies against synthetic presequence polypeptides specific to nuclear-encoded subunit IV precursor protein of rat brain cytochrome oxidase. We found that the precursors were located not only in neuronal cell bodies, but also in dendrites and axon terminals. This indicates that the conversion of these precursors to their mature form is not confined to the cell body but occurs in dendrites and axons as well. At the electron microscopic level, an overwhelming majority of immunoreaction product was found within mitochondria, suggesting that precursor proteins are transported to neuronal processes mainly within mitochondria, and that their half-lives are much longer in neurons than in yeast and rat hepatocytes. The precursor pool was downregulated in the rat superior colliculus after monocular enucleation, indicating that precursor synthesis and/or degradation is regulated by neuronal functional activity. These results also suggest that local functional demands may play an important role in controlling the processing of precursors and the assembly of holoenzymes in dendrites and axon terminals. This allows neurons to regulate enzyme levels locally, precisely, and rapidly.