Respiratory motor outputs contain medium-(MFO) and high-frequency oscillations (HFO) that are much faster than the fundamental breathing rhythm. However, the associated changes in power spectral characteristics of the major respiratory outputs in unanesthetized animals during the transition from normal eupneic breathing to hypoxic gasping have not been well characterized. Experiments were performed on 9 unanesthetized, chemo- and baro-denervated, decerebrate adult rats, in which asphyxia elicited hyperpnea followed by apnea and gasping. A gated Fast Fourier transform (FFT) analysis and a novel time-frequency representation (TFR) analysis were developed and applied to whole phrenic and to medial branch hypoglossal nerve recordings. Our results revealed one MFO and one HFO peak in the phrenic output during eupnea, where HFO was prominent in the first two-thirds of the burst, and MFO in the latter two-thirds of the burst. The hypoglossal activity contained broad-band power distribution with several distinct peaks. During gasping, two high-amplitude MFO-peaks were present in phrenic activity, and this state was characterized by a conspicuous loss in HFO power. Hypoglossal activity showed a significant reduction in power and a shift in its distribution towards lower frequencies during gasping. TFR analysis of phrenic activity revealed the increasing importance of an initial low-frequency "start-up" burst that grew in relative intensity as hypoxic conditions persisted. Significant changes in MFO and HFO rhythm generation during the transition from eupnea to gasping presumably reflect a reconfiguration of the respiratory network and/or alterations in signal processing by the circuitry associated with the two motor pools.