The entorhinal cortex (EC) is a medial temporal lobe area involved in memory consolidation. Results from previous studies suggest that the upper layers of the EC may be organized into anatomical-neurochemical modules associated with pathways through the neuron clusters in layers II and III. To study metabolic patterns in the EC and to look for correlates of the proposed modules, we examined the distribution of cytochrome oxidase (CO) in the human, monkey, and rat EC. CO is a mitochondrial enzyme that has been used to study modules in other cortical areas. In all three species, the neuron clusters in layers II-III were darkly CO-reactive, whereas most of the neuropil between clusters was lightly or moderately CO-reactive. However, some neuropil regions directly adjacent to the neuron clusters were also darkly CO-reactive, especially in the human; these neuropil areas included portions of layers I and II. In tangential sections through layers I-II, the areas of dark staining formed a consistent pattern, comprised of partially interconnected islands and stripes associated with the neuron clusters. In the EC from one human hemisphere, approximately 200-250 CO-reactive layer II islands were present. EC layers other than I-III also showed characteristic CO staining intensities, but no evidence of modularity. Our results indicate that CO staining labels distinct compartments related to the neuron clusters in the upper EC layers. We propose that these compartments may represent modules for cortical processing, analogous to the CO-labeled modules in some other areas of cortex.