OBJECTIVE: We evaluated the activity of autonomic nervous system in children with celiac disease by using heart rate variability (HRV) analysis. METHODS: HRV parameters of 37 children with celiac disease were compared to 36 age- and sex-matched healthy controls. None of the participants had a systemic, central or peripheral neurological disease. RESULTS: Statistically significant differences were present in two parameters; standard deviation of all RR intervals (SDNN) and standard deviation of 5-minute RR interval means (SDANN). Age was negatively correlated with mean, minimum and maximum heart rate. Duration of disease was positively correlated with low frequency power-high frequency power ratio. No correlation was found between anti-tissue transglutaminase IgA level and HRV parameters. CONCLUSIONS: Celiac disease may affect autonomic nervous function in children even if there are no symptoms of dysautonomia.