The aim of the present study was to investigate the effect of hypercapnia and hypoxia on apnea and non-nutritive swallowing (NNS) frequency as well as on the coordination between NNS and phases of the respiratory cycle in newborn lambs, whilst taking into account the potential effects of states of alertness. Six lambs were chronically instrumented for recording electroencephalogram, eye movements, diaphragm and thyroarytenoid muscle (a glottal adductor) activity, nasal airflow and electrocardiogram. Polysomnographic recordings were performed in non-sedated lambs exposed to air (control), 10% O₂ and 5% CO₂ in a random order at 3, 4 and 5 days of age. While hypercapnia decreased apnea frequency in wakefulness and active sleep (p = 0.002 vs. air and hypoxia), hypoxia had no significant effect on apnea. In addition, while hypercapnia increased NNS frequency during wakefulness and quiet sleep (p < 0.005 vs. air and hypoxia), hypoxia tended to decrease the frequency of NNS. Finally, only hypercapnia altered NNS-breathing coordination by increasing NNS occurring at the transition from inspiration to expiration (ie-type NNS) (p < 0.001 vs. air and hypoxia). In conclusion, whereas hypercapnia increases overall NNS frequency by specifically increasing ie-type NNS, hypoxia has the inverse tendency. Results were identical in all three states of alertness.