BACKGROUND: Children with intractable epilepsy have chronic dysfunction of the autonomic nervous system causing myocardial ischemia. Heart-type fatty acid-binding protein (H-FABP) is a sensitive biomarker for myocardial ischemia. AIMS: We aimed to evaluate serum levels of H-FABP during seizures compared to their interictal levels and healthy controls and changes in heart rate (HR) and HR variability (HRV) in epileptic children with intractable seizures. MATERIALS AND METHODS: We included 30 epileptic seizures in 25 children with intractable epilepsy and 30 matched controls. They were subjected to video-electroencephalography monitoring simultaneously with Holter electrocardiogram and measurement of H-FABP. RESULTS: Mean serum levels of H-FABP were increased significantly in patients either in the ictal or interictal periods compared to that in the controls (P < 0.001 and P< 0.01, respectively). There is no significant difference in serum levels of the H-FABP in the ictal and interictal periods. The basal time domain measures of HRV were significantly lower in the patient group compared to the control group. CONCLUSION: H-FABP might suggest a degree of myocardial ischemia in intractable epilepsy. HRV is impaired in patients with refractory seizures.