OBJECTIVE: Heart rate variability (HRV) measures are altered in various cardiac and non-cardiac situations in children. The autonomic nervous system is assumed to have a role in the pathophysiology of atrial septal defect (ASD). In this study, we evaluated the autonomic system by measuring HRV in children with ASD. METHODS: Twenty-eight patients with ASD and 32 healthy children (mean ages: 6.6+/-2.1 years and 6.4+/-2.2 years, respectively) were enrolled in the study. Twenty-four-hour ambulatory electrocardiographic recordings were obtained and the seven time-domain (SDNN, SDANN, rMSSD, SD, SDNN index, PNN50, and mean RR) and four frequency-domain (VLF, LF, HF, and LF/HF ratio) indices of HRV were analyzed. RESULTS: A significant decrease in calculated HRV variables was observed in children with ASD as compared to controls. The HRV alteration was found in both time-domain and frequency-domain parameters. CONCLUSIONS: Our results indicate that HRV is decreased in children with ASD, which implies parasympathetic withdrawal and sympathetic predominance.