Abstract Objective To measure the level of hair Mg, as well as its level in serum, in patients with epilepsy and compare them to the levels found in non-epileptic age and gender matched children, and to explore any potential correlation between either serum or hair level of magnesium and seizure characteristics in children with idiopathic epilepsy. Methods An observational cross-sectional study including 50 children with idiopathic epilepsy and 100 non-epileptic age and gender matched control subjects. Cases were subjected to full history taking, examination and measurements of serum and hair levels of magnesium, control subjects only had their serum and hair level of magnesium measured as for the cases. Results The mean serum magnesium was 29.11 ± 13.42 ug/ml for cases and 27.67 ± 7.24 ug/ml for controls and the median hair level of magnesium was 42.22 ug/g with IQR of 25.9 - 56.82 for cases and 38.6 ug/g with IQR of 25.21 - 61.25 for controls. No statistically significant difference was observed between both groups as regards either serum or hair magnesium levels. No statistically significant correlation was observed between either hair or serum levels of magnesium and seizure characteristics though the correlations were nearing statistical significance for the hair magnesium content. Conclusion Hair magnesium level may be better correlated to seizure characteristics and control than serum levels in patients with epilepsy.