A decreased arousability and an increased risk for sudden infant death syndrome (SIDS) have been shown in infants sleeping prone. Obstructive apnea, a known risk factor for SIDS, is less often terminated by an arousal reaction in infants than in adults. The effect of body position on the arousal reaction to spontaneous respiratory events had not been previously studied in infants. The aim of our study was to see if body position has an influence on the frequency and delay of the arousal reaction to obstructive apnea. All obstructive events recorded during two successive nights in 20 infants sleeping one night prone and one night supine were studied. During the supine recording 153 obstructive events were detected, and 217 were detected during the prone session. Prone sleep was not associated with an increased frequency of obstructive apneas. Total sleep time was 382 min (range, 283-456) supine and 423 min (range, 325-521) prone (p = 0.003). Obstructive events duration was 6.5 s (range, 3-21.5) when sleeping supine and 8 s (range, 3.5-30.5) when prone (p = 0.002). Behavioral arousal were found in 57.5 % of obstructive events recorded supine and in 31.3 % of those seen prone (p < 0.001). Arousal occurred after 8 s (range, 0-21) from the start of the obstructions when supine and 10.5 s (range, 3.5-23.5) when prone (p = 0.001). Sighs were found in 34 % of supine obstructive events and in 44.7 % of those prone (p = 0.040). A reaction, i.e. arousal or sigh, was found in 91.5 % of supine events and 76 % of those prone (p < 0.001). We conclude that when sleeping supine, infants arouse to obstructive events more often and after shorter delay than when prone.