The chemical neuroanatomy of breathing must ultimately encompass all the various neuronal elements physiologically identified in brainstem respiratory circuits and their apparent aggregation into "compartments" within the medulla and pons. These functionally defined respiratory compartments in the brainstem provide the major source of input to cranial motoneurons controlling the airways, and to spinal motoneurons activating inspiratory and expiratory pump muscles. This review provides an overview of the neuroanatomy of the major compartments comprising brainstem respiratory circuits, and a synopsis of the transmitters used by their constituent respiratory neurons.