OBJECTIVE: The autonomic nervous system is assumed to have a role in the pathophysiology of obesity. In this study, we evaluated the autonomic system by measuring heart rate variability (HRV) in obese children. METHODS: Thirty-two obese and 30 healthy children (mean ages: 11.6+/-2.0 years and 11.0+/-2.9 years, respectively) were enrolled in the study. Obesity was defined as a body mass index higher than 97th percentile for age- and gender-specific reference values. All participants were free of any disease and none of them was receiving any medication. Twenty-four-hour ambulatory electrocardiographic recordings were obtained and the time-domain and frequency-domain indices of HRV were analyzed. The study group was evaluated with respect to insulin resistance by HOMA-IR values. RESULTS: A significant decrease in calculated HRV variables was observed in obese children as compared to controls. The HRV alteration was found in both time-domain and frequency-domain parameters. The subgroup analysis of the study group revealed a significant decrease in all investigated HRV parameters in the insulin-resistant obese children compared to the non-insulin-resistant obese ones. CONCLUSIONS: Our results indicate that HRV is decreased in obese children, which implies parasympathetic withdrawal and sympathetic predominance. A marked decrease in HRV was observed in insulin-resistant obese children compared to their non-insulin-resistant counterparts. We propose that autonomic imbalance pertaining especially to insulin resistance may be involved in the pathogenesis of obesity in pediatric patients.