Neuroscientists have long sought to understand how circuits in the nervous system are organized to generate the precise neural outputs that underlie particular behaviors. Recent studies deepened our understanding of the mechanisms responsible for the generation of the rhythmic output for breathing. Here, the author focuses on issues that are pertinent for the respiratory network and considers its organization and how it derives the functional output. The author discusses pacemaker and network mechanisms of rhythm generation, which are now combined into a novel concept of emergent network activity due to coherent excitation of pacemaker groups. He discusses subcellular basis of this hypothesis and possible mechanisms of synchronization within respiratory network. These new findings in respiratory neuroscience are further applied to explain modifications in breathing during hypoxia and possible origins of respiratory disorders that may be acquired during neural development and aging.