In this study, serum triglyceride, total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (HDL-C), very low-density lipoprotein cholesterol (VLDL-C), vitamin B12 and folic acid levels were studied in children with epilepsy who had been receiving long-term valproate (VPA) therapy. Our purpose was to determine that whether or not there was any affect of VPA therapy on serum lipids, vitamin B12 and folic acid levels. The study includes 26 patients (13 males, 13 females) with epilepsy who had been receiving long-term VPA therapy and in 28 healthy children (14 males, 14 females). The age ranged from 14 months-12 years (8.22 +/- 3.64 years) and 9 months-18 years (8.97 +/- 4.85 years) in the study and control group, respectively. Because serum lipid ranges may be changed according to the age groups in childhood, the children were divided into three groups as follows; younger than < 5 years, between 5-10 years, and older than > 10 years. The duration of VPA use was between 10 months and 7 years (1.83 +/- 1.80 years). Serum VPA level changed between 42-108 mug/ml (75.09 +/- 21.42 mug/ml). When comparing the results we did not find any significant difference in all parameters including lipid profiles, vitamin B12 and folic acid levels between the groups (P > 0.05). Additionally, we did not find any correlation between lipid profile and age at start of therapy, duration of therapy, serum VPA level (P > 0.05). In conclusion, our findings showed that VPA therapy did not change serum lipids, vitamin B12 and folic acid concentrations; therefore, we suggest that VPA may be safely used with regard to lipid composition, vitamin B12 and folic acid levels in childhood epilepsy.