Background and Objective: Chronic use of antiepileptic drugs may influence the bones and their mineral metabolism due to deficiency of vitamin D3. In this study we investigated the effect of high dose vitamin D3 on bones and their mineral metabolism. Materials and Methods: Fifty six children older that 3 years old who were affected by epilepsy and had taken the antiepileptic drugs at least for 6 months were included in the study. Levels of alkaline phosphatase (ALP), calcium, phosphorus and vitamin D3 was measured. The patients were divided into three groups one group was provided with 1peril of 50000 units of vitamin D and the other two groups took 2 and 3 perils of vitamin D. Two months after prescription, serum level of the above parameters were measured and compared with the results before vitamin D prescription. Results: After prescription of vitamin D3, decrease of ALP (p<0/001), increase of calcium (p=0/01) and increase level of vitamin D3 in serum (p<0/001) was observed. The highest increase in the serum level of vitamin D3 was observed in the group which had received 3 perils of vitamin D (p<0/0001). Conclusion: Decrease in the serum level of vitamin D3 following long term use of antiepileptic drugs and its increase as a result of vitamin D supplementation suggests that this method of therapy can prevent the skeletal abnormalities due to side effects of these drugs.