The neuronal network controlling breathing under in vivo conditions is a distributed throughout the lower brainstem and the pons. Responsible for the respiratory rhythm generation is a core micro-circuitry formed within the pre-Bötzinger Complex (pre-BötC) and the Bötzinger complex (BötC) regions. A basic process is executed by glycinergic neurons forming a distinct inhibitory connectome between early-inspiratory, post-inspiratory and also late-expiratory neurons. It generates an effective control of endogenous bursting activity and allows a dynamic adjustment of breathing to behavioral and cortical commands. Disturbances of this neural management may become dangerously life threatening as they can lead to an abnormally prolonged inspiration (apneusis) producing enduring breath-holdings and also to complete cessation of breathing (apnea). Comparable defects of glycinergic inhibition were identified in several diseases, such as in Rett Syndrome, Hyperekplexia, Olivo-ponto-cerebellar atrophy (OPCA) and also Brainstem infarction. The systemic processes underlying such disorder of respiratory activity will be explained by a comparative analysis of the effects of modulation or depression of glycinergic inhibition on single cell responses and computational modeling of complex network reactions.