Cytochrome oxidase (CO) is a mitochondrial energy-generating enzyme of the oxidative phosphorylation pathway. In neurons, CO activity varies among different cells and compartments (perikarya, dendrites, axons, and terminals) according to their physiological activity and metabolic requirements. Regulation of enzyme protein levels, rather than enzyme turnover number, largely accounts for local variations in CO activity (Hevner and Wong-Riley, 1989, 1990). In the present study, we examined how CO activity and protein levels are related to mitochondrial DNA (mtDNA) and CO subunit mRNA levels in neurons and neuronal compartments. Mammalian CO comprises 13 subunits (Kadenbach et al., 1983), of which three are encoded in mtDNA and 10 in nuclear genes. We studied one mitochondrial-encoded mRNA [subunit I (COI)], two nuclear- encoded mRNAs (COIV, COVIII), and mtDNA, using in situ hybridization to determine their distributions in monkey hippocampus, cerebellum, and primary visual cortex. We compared their distributions with those of CO activity and protein, determined by histochemistry and immunohistochemistry, respectively. In all regions, the local content of mtDNA was similar, but not identical, to the activity and amount of CO. Expression of COI mRNA was not proportional to mtDNA abundance or CO activity and protein, but instead was highest in cell bodies, lower in dendrites, and undetectable in axon terminals. COIV and COVIII mRNAs were detected exclusively in perikarya and proximal dendrites. Thus, the nuclear-encoded subunits of CO are probably translated mainly in neuronal cell bodies and allocated to other compartments posttranslationally. Regulation of CO was studied in two monkeys treated by monocular tetrodotoxin (TTX) injection, a procedure that blocks impulses from one eye. In those animals, cortical changes in CO activity were correlated with changes in mtDNA and in COI, COIV, and COVIII mRNA. Our results suggest that neuronal CO is synthesized and assembled mainly in cell bodies and indicate that both nuclear and mitochondrial CO subunit genes are regulated by neuronal activity.