The recent demonstration that certain mitochondrial subunits of cytochrome oxidase (CO) are regulated by neuronal activity has stimulated interest in the molecular processes that coordinate nuclear and mitochondrial gene expression following synaptic stimulation. We have studied the constitutive expression and activity-guided regulation of cytochrome b (cyt b), a gene that is encoded by mitochondrial DNA and that was cloned by subtractive hybridization from the lateral geniculate nucleus in the monkey. We have found cyt b mRNA expression in monkey striate cortex to be similar to that of CO activity with regard to the laminar profile and the presence of blobs in the supragranular layers. Layers 2/3, 4C, and 6 contained large numbers of stained cells, many of which were judged to be excitatory neurons, because they showed a Zif268-immunopositive nucleus. We have also found that removal of functional activity reduced cyt b mRNA content in area V1. Columns of reduced cyt b staining were visible after 3 days and were especially striking after 6 days of monocular deprivation. After 3 months of deprivation, the columns lost their contrast and became blurred. Our principal finding, that neuronal activity regulates cyt b levels, suggests that expression of a mitochondrial gene can be affected in a manner similar to that of several known nuclear genes. The differences in cyt b mRNA levels and CO activity after long-term deprivation suggests that some form of differential control is exerted on cyt b. Cyt b expression, therefore, may be used as a marker of altered mitochondrial transcription that is guided by the metabolic demands of active neurons.