Antiepileptic drugs (AED) had an effect on bone metabolism in children. This study was conducted in order to determine the relationships between serum leptin levels, bone mineral density (BMD) and bone turnover markers in epileptic children. Fifty-three patients were treated with valproic acid (VPA) and 23 with carbamazepine (CBZ) monotherapy; 50 healthy children were included in the study as controls. Serum alkaline phosphatase (ALP) and cross-linked C-telopeptide (CTx) levels were statistically significantly higher in the CBZ group than in the VPA group and the control group (p < 0.0001, p < 0.010, respectively). Serum osteocalcin and ALP levels were significantly lower in the VPA group than in the control group (P < 0.012, P < 0.030, respectively). Although we found slightly higher serum leptin levels in both the CBZ and VPA groups, they were not significantly different from the control group (P > 0.05). We demonstrated that the markers of bone formation and resorption increased with CBZ and decreased with VPA treatment without affecting BMD and vitamin D levels in prepubertal epileptic children.