We have developed the Subcellular Anatomy Ontology for the Nervous System (SAO) to provide a formal ontology to describe structures from the dimensional range known as the “mesoscale,” encompassing cellular and subcellular structure, supracellular domains, and macromolecules. The SAO describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.