Upper airway stabilizing muscles play a crucial role in the maintenance of upper airway patency. Transcranial magnetic stimulation allows the investigation of the corticomotor activation process for respiratory muscles. This technique has also been used to evaluate the genioglossus corticomotor response. The aims of this study were to characterize the response of different upper airway stabilizing muscles to focal cortical stimulation of the genioglossus. Alae nasi, genioglossus, levator palatini, palatoglossus and diaphragm motor-evoked potential responses to transcranial magnetic stimulation were recorded during expiration, tidal inspiration and deep inspiration in nine normal awake subjects. A concomitant response of the four studied upper airway muscles was observed in the majority of cortical stimuli. The response of these muscles was independent of the diaphragmatic one that was only occasionally observed. Significant positive relationships were found between alae nasi, levator palatini and palatoglossus motor-evoked potential latencies and amplitudes and the corresponding values of the genioglossus. We conclude that transcranial magnetic stimulation applied in the genioglossus area induces a concomitant motor response of upper airway stabilizing muscles with consistent changes in their motor responses during inspiratory manoeuvres.