AIMS: To assess the autonomic function in infants with idiopathic apparent life threatening event (IALTE) with and without gastroesophageal reflux (GER) and to compare the autonomic activity in events of pure obstructive apnea and coupled events of apnea associated with GER. METHODS: Seventeen infants diagnosed with IALTE and GER and 17 matched infants with IALTE only between the ages of 3-28 weeks participated in the study. All infants underwent a polysomnography including esophageal pH measurements. Obstructive apneas with and without associated GER were identified. Heart rate variability (HRV) was evaluated employing time domain analysis for short- and long-term variability. Forty R-R intervals for each epoch preceding, during, and following the episodes, as well as 10 segments of 40 R-R intervals unrelated to apneic episodes were analyzed. RESULTS: A decreased baseline short-term variability among infants with IALTE and GER was found. Both short- and long-term variability were significantly increased in the period preceding the obstructive apnea when compared to the baseline values. No such autonomic activity was observed preceding coupled events of apnea and GER. While a significant increase in long-term variability following an obstructive apnea when compared to the apnea period was observed, no such changes were found following a coupled apnea-GER event. CONCLUSIONS: Infants with history of IALTE and GER have a significant abnormality in their autonomic control that is marked in the coupled events of apnea and GER. This finding is possibly related to medullary autonomic regulation.