Long-term treatment with some older antiepileptic drugs may lead to dyslipidemia or thyroid disturbances. The effect of levetiracetam (LEV), a newer broad spectrum antiepileptic agent, on cardiovascular risk factors is not yet sufficiently investigated. The purpose of this study was to investigate prospectively the effect of LEV monotherapy on serum lipid profile and thyroid hormones levels in children with epilepsy. The study population consisted of 39 children (21 females, 18 males, mean age 6.8 ± 4,1 years, range 2–15 years) that were treated for new-onset epilepsy with LEV monotherapy. Serum total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides (TGs), apolipoprotein A–I (apo A–I), apolipoprotein B (apo B), lipoprotein (a) [Lp(a)], thyroxine (T4), free thyroxine (FT4) and thyrotropin (TSH), were evaluated before and at 6 and 12 (n = 28) months of LEV monotherapy. TGs were significantly decreased at 6 and 12 months of LEV treatment (p = 0.026 and p = 0.001, respectively). TGs/HDL-C ratio was significantly decreased at 6 and 12 months of LEV treatment (p = 0.024 and p = 0.003, respectively), while LDL-C/HDL-C ratio was significantly decreased at 12 months of LEV treatment (p = 0.025). There were no significant alterations in the other parameters during the study. In conclusion, long-term LEV monotherapy does not cause adverse alterations on thyroid hormones and serum lipids in children with epilepsy. More studies are needed to clarify whether LEV monotherapy have a favourable effect on serum lipids and whether LEV may be considered as a safer alternative drug for the prevention of antiepileptic drug-induced cardiovascular complications in adult life.