Neonatal apnea is characterized by decreased neural output to the ventilatory muscles, and frequently associated with upper airway obstruction. We sought to characterize: (1) the role of central chemosensitive structures at the ventral medullary surface (VMS) in modulating hypoglossal and phrenic neural output, and (2) the recovery of hypoglossal and phrenic neural output during simulated central apnea. We studied 14 anesthetized, paralyzed, ventilated piglets aged 14-21 days and performed VMS cooling to inhibit central neural pathways mediating CO2 sensitivity. Phrenic and hypoglossal ENGs and end-tidal CO2 were continuously recorded. During CO2 rebreathing, hypoglossal activity was always more sensitive than phrenic activity to the inhibitory effects of VMS cooling. When phrenic apnea was induced by VMS cooling, and followed by discontinuation of ventilation for 60 sec in order to induce simultaneous hypercapnia and hypoxia, reappearance of hypoglossal ENG was delayed and recovery was significantly suppressed when compared to phrenic ENG. Therefore, attenuated central chemosensitivity during early postnatal life appears to preferentially inhibit neural output responsible for upper airway patency, and may predispose to upper airway obstruction during recovery from neonatal apnea.