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Summary: Purpose: Autonomic symptoms frequently occur during seizures. There are reports that the adult group of intractable epilepsy patients have different autonomic profile than the well controlled epilepsy, but there is no clear evidence in the children epilepsy group, therefore, we planned to study the autonomic profile in well controlled and refractory epilepsy children by recording the short-term heart rate variability (HRV). Methods: This cross sectional study was conducted in a tertiary care hospital between July 2008 and June 2009. Children with mean age of 9.1±3.3 years were enrolled. Three groups of children, 40 in each group namely, refractory epilepsy, well controlled epilepsy and normal control children were included. Children who had chronic systemic diseases and were on drugs that cause autonomic dysfunction were excluded. All children underwent short term heart rate variability testing. Data was analyzed in time domain and frequency domain. Results: pNN50 was significantly lower in children with refractory epilepsy than the well control as well as healthy controls. Rest of the parameters of time domain and frequency domain were comparable between the groups. Conclusions: Our study showed that parasympathetic activity is lower in refractory epilepsy children. However, autonomic tone is comparable in well control versus healthy controls. [Copyright &y& Elsevier]