Abstract Inspiratory (I) discharges of the phrenic (Phr) and glossopharyngeal (stylopharyngeal muscle branch, IX) nerves were compared in the urethane anesthetized, vagi-intact and artificially ventilated rat in which respiratory rhythm was generated in synchrony with cyclic changes in airway pressure (P aw) produced by a ventilator. Observations were made during respiratory suppression due to excess lung inflation and bilateral cooling of the ventral medullary surface (VMS). In the control condition, regular rhythmic I bursts appeared at low baseline P aw phase (lung deflation) and ceased when P aw increased (lung inflation) in each ventilator cycle. Increase in baseline P aw (P aw > 8 cmH 2O, excess lung inflation) suppressed the initiation of rhythmic I discharge. However, threshold baseline P aw for suppressing I bursts was higher in the IX than in the Phr nerve, and regular rhythmic I activity remained in the IX even after cessation of Phr bursts. During VMS cooling, I bursts disappeared first in the Phr and subsequently in the IX nerve and emerged always first in the IX during recovery. The results suggest that I activity of the IX (stylopharyngeal) motoneurons, which are located in the rostral part of the nucleus ambiguus, are less suppressed than that of Phr motoneurons by vagal afferents arising probably from slowly adapting pulmonary stretch receptors or by a reduction in respiratory drive from VMS. These differential responses of Phr and IX motoneurons may be ascribed to differences in activation or inhibition processes between two motoneuron groups despite both being driven by a common rhythm generator.