Fast respiratory rhythms include medium- (MFO) and high-frequency oscillations (HFO) which are much faster than the fundamental breathing rhythm. According to previous studies, HFO is characterized by high coherence (Coh) in phrenic (Ph) nerve activity, thereby providing a means of distinguishing between these two types of oscillations. Changes in Coh between the Ph and hypoglossal (XII) nerves during the transition from normal eupnic breathing to gasping have not been characterized. Experiments were performed on 9 unanesthetized, chemo- and baro-denervated, decerebrate adult rats, in which sustained asphyxia elicited hyperpnea and gasping. A gated time-frequency coherence analysis was developed and applied to whole Ph and medial XII nerve recordings. The results showed dynamic Ph-Ph coherence during eupnea, including MFO and HFO. XII-XII Coh during eupnea was broad-band, and included four distinct peaks, with low frequency Coh dominating the epochs preceding the onset of Ph activity. During gasping, only MFO-peaks were present in Ph-Ph Coh. Bilateral XII activity showed a significant reduction in Coh and a shift towards lower frequencies during gasping. In contrast, contralateral Ph-XII Coh progressively increased during state changes from eupnea to gasping, a tendency mirrored in the start-up part of the Ph activity. These data suggest significant hypoxia/hypercapnia-induced alterations in synchronization between respiratory outputs during the transition from eupnea to gasping, reflecting a reconfiguration of the respiratory network and/or alterations in the circuitry associated with the motor pools, including dynamic coupling between outputs.