We intended to evaluate the carotid intima-media thickness (CA-IMT) as a surrogate factor for atherogenesis in epileptic patients on enzyme inducer (EI) antiepileptic drugs (AEDs) or valproate (VA). The study included 71 patients with epilepsy (37 females) aged 27.7 ± 8.1 and 71 age- and sex-matched non-epileptic subjects. Patients with history of at least 2 years antiepileptic treatment were enrolled. Subjects with known history of cardiovascular risk factors were not included. Thirty-eight patients (21 females) were treated with EI medications and 33 (16 females) with VA. CA-IMTs were measured by a single sonography system in all participants. CA-IMT values were compared between patients with epilepsy and the controls and within the patients with epilepsy on VA or EI medications. Duration of epilepsy was 10.1 ± 7.1 years. Patients were treated with their current AED for 6.9 ± 4.8 years. The CA-IMT of patients with epilepsy was higher than non-epileptic control subjects on either left (0.502 ± 0.079 vs. 0.470 ± 0.073 mm; p = 0.012) or right side (0.524 ± 0.078 vs. 0.458 ± 0.068 mm; p < 0.001). Patients on VA were younger than those receiving EI medications (25.8 ± 7.1 vs. 29.4 ± 8.7 years). Age adjusted CA-IMT values of patients on VA did not differ from the values of patients receiving EI medications. Duration of drug administration did not correlate with CA-IMT values. Patients with epilepsy on AEDs are at higher risk for atherogenesis. In the population of this study the increased risk of atherogenesis was not attributable to the administered AED or duration of treatment.