The relationship between migraine and epilepsy has been previously investigated in the literature. Several pathogenetical hypotheses have related the two conditions including the suggestion of a common genetic origin. The purpose of our study was to analyze the rate of migraine in our epileptic children population from Southern Italy followed-up at our unit between 2002 to 2005. Clinical data were retrospectively obtained from the patients' medical records. Migraine was far more frequent in subjects with idiopathic or cryptogenic epilepsy vs. non-epileptic controls with a 16.5 times higher risk ratio in the subjects with idiopathic or cryptogenic epilepsy vs. controls. The group of patients with partial seizures had five-fold increased risk to have migraine compared to the group with generalized seizures. The plausible pathogenetic relationship between migraine and epilepsy needs to be further investigated in wider populations. The detection of a common background could provide evidence for a common and more effective pharmacological treatment of these two disorders.