The aim of this study was to determine if episodic hypoxia evokes persistent increases of genioglossus muscle (GG) activity, termed long-term facilitation (LTF), in neonatal rats in vivo. Experiments were performed on anaesthetised spontaneously breathing intubated neonatal rats (P3 - 7), divided into 3 groups. The first group (n = 8) was subjected to three, 5-minute periods of hypoxia (5% O₂, 95% N₂) alternating with 5-minute periods of room air. The second group (n = 8) was exposed to 15 minutes of continuous hypoxia. The third (n = 4) group was not exposed to hypoxia and served as a control. GG EMG activity and airflow were recorded before, during and for 60 minutes after episodic and continuous hypoxic exposure. During hypoxia, GG EMG burst amplitude and tidal volume (V_T) significantly increased compared to baseline levels (episodic protocol: mean±S.E.M; 324±59 % of control and 0.13±0.007 vs 0.09±0.005 ml respectively; continuous protocol: 259±30 % of control and 0.16±0.005 vs 0.09±0.007 ml respectively; p < 0.05). After the episodic protocol, GG EMG burst amplitude transiently returned to baseline; over the next 60 minutes, burst amplitude progressively increased to levels significantly greater than baseline (238±40 % at 60 minutes; p < 0.05), without any significant increase in VT and respiratory frequency (p > 0.05). After the continuous protocol, there was no lasting increase in GG EMG burst amplitude. We conclude that LTF of upper airway muscles is an adaptive respiratory behaviour present from birth.