The aim of this study was to determine the alterations in thyroid function during carbamazepine or valproate monotherapy in a prospective study. Forty patients treated with valproate, 33 patients treated with carbamazepine, and 36 control patients, all aged between 2 and 18 years, were enrolled in our study. Serum levels of thyroid hormones were measured before the beginning of the antiepileptic therapy and at 6 and 12 months of treatment. Carbamazepine-treated patients showed mean serum thyroid hormone levels significantly lower than baseline evaluation and the control group. Thyroid-stimulating hormone levels at 6 and 12 months were not significantly different in carbamazepine treated patients. Serum hormone levels did not change during valproate treatment. Thyroid-stimulating hormone levels were significantly higher at the 12th month of valproate treatment. Our data suggest that although carbamazepine causes significant alterations in thyroid hormone levels, these changes do not lead to clinical symptoms at the follow-up period of 12 months.