Diagnostic examinations (laboratory findings, electroencephalogram (EEG) and neuro imaging techniques) should complete the medical history and confirm the clinical suspicion of epilepsy. However, we believe that some other biomarkers also help early diagnosis of epilepsy which enables timely initiation of treatment and finally, the possibility of better life quality. Apolipoprotein E as a biomarker takes part in many metabolic processes in the brain and, therefore, considering the plasticity of the brain in children, it could play an important role in children suffering from epilepsy. The main goal of this research is to determine whether there is a difference between particular types and sub-types of epilepsy depending on the APOE gene polymorphism in children. The shares of APOE gene polymorphisms are compliant with the data of European studies showing that the e3/e3 genotype is equally distributed in children suffering from epilepsy and general population. The earlier onset and more severe clinical picture of the disease are expected in persons with APOE polymorphism. Other factors, such as the age at seizure onset, seizure frequency, impact on neuromotor development and later on the lifestyle are more important for predicting the course of the disease. When diagnosing and classifying epilepsy it is not necessary to use the APOE genotyping.