BACKGROUND: The aim is to determine the effects of antiepileptic drugs (AEDs) on serum folic acid (FA) and vitamin B12 (B12) in epileptic children, and to investigate the related factors contributing to the change of the serum levels. METHODS: The levels of serum FA and B12 were measured before the start of AEDs and at the 6-12 months intervals in epileptic children receiving AEDs for at least 1-year period between Jan 2014 and Mar 2017. The difference of FA and B12 levels between before the treatment and the last follow-up were compared and analyzed. RESULTS: 154 children (98 boys, 56 girls) with the mean age of 7.3±5.1 years were included. The mean follow-up duration was 1.7±0.7 years. Serum FA in patients decreased significantly (−3.5±4.6 ng/mL; 16.2±5.1 vs 12.7±5.3 ng/mL, P0.001) during follow-up period, however, B12 level was increased, not statistically significantly (88±153 pg/mL; 925±331 vs 1015±514 pg/mL, P=0.264). At the start of AEDs and the last follow-up, FA deficiency (≤8 ng/mL) was recognized in 6.5% (10/154) and 26.6% (41/154), respectively ( P0.001). Polytherapy (−4.8±4.7 vs −2.6±4.4 ng/mL, P=0.004), longer duration of AEDs (−6.2±4.7 vs −1.7±3.7 ng/mL, P0.001), tube feeding (−6.8±5.4 vs −3.2±4.4 ng/mL, P =0.005), and ketogenic diet (−8.2±2.2 vs −3.1 ±4.6 ng/mL, P0.001) had a significant negative effect for the longitudinal change of FA. Age, gender, brain lesion, seizure outcomes, and overweight were not related to the decrease of FA levels. B12 levels were significantly increased in children treated with valproate compared with other AEDs ( P=0.031). CONCLUSIONS: The medication of AEDs can be associated with reduced serum FA levels in epileptic children. Polytherapy, longer duration of AEDs, tube feeding, and ketogenic diet may be risk factors for longitudinal decrease of FA levels.