Nerve fibres in the larynx detect foreign substances and elicit a stereotypical airway protective response that can be simulated by electrical stimulation of the superior laryngeal nerve (SLN). In humans the response includes cough, swallowing and a cessation of breathing (apnoea). It is still unknown precisely how the central nervous system coordinates swallowing and breathing, and at which point the two vital systems converge and diverge in the brain. Here we report a temporal, sequential relationship between excitation of expiratory laryngeal motoneurons that close the larynx during swallowing, and inhibition of breathing, during stimulation of the SLN in rat. The two phenomena can be dissociated by inactivating different brain areas. This work therefore has implications for diseases such as sudden infant death syndrome and Parkinson's disease, in which incoordination of breathing and protective behaviours may result in aspiration of irritants and subsequent death or aspiration pneumonia. Abstract A striking effect of stimulating the superior laryngeal nerve (SLN) is its ability to inhibit central inspiratory activity (cause 'phrenic apnoea'), but the mechanism underlying this inhibition remains unclear. Here we demonstrate, by stimulating the SLN at varying frequencies, that the evoked non-respiratory burst activity recorded from expiratory laryngeal motoneurons (ELMs) has an intimate temporal relationship with phrenic apnoea. During 1-5 Hz SLN stimulation, occasional absences of phrenic nerve discharge (PND) occurred such that every absent PND was preceded by an ELM burst activity. During 10-20 Hz SLN stimulation, more bursts were evoked together with more absent PNDs, leading eventually to phrenic apnoea. Interestingly, subsequent microinjections of isoguvacine (10 mm, 20-40 nl) into ipsilateral Bötzinger complex (BötC) and contralateral nucleus tractus solitarii (NTS) significantly attenuated the apnoeic response but not the ELM burst activity. Our results suggest a bifurcating projection from NTS to both the caudal nucleus ambiguus and BötC, which mediates the closely related ELM burst and apnoeic response, respectively. We believe that such an intimate timing between laryngeal behaviour and breathing is crucial for the effective elaboration of the different airway protective behaviours elicited following SLN stimulation, including the laryngeal adductor reflex, swallowing and cough.