Lennox-Gastaut (LGS) syndrome is an epileptic encephalopathy characterized by different types of seizures, typical EEG changes and mental retardation. Purpose: Simultaneous electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) recording is a non-invasive tool for investigating epileptogenic networks. The purpose of this study was to investigate EEG-fMRI in children suffering from LGS. Methods: 20 children with LGS and focal epilepsy were recruited and underwent a 20-min EEG-fMRI acquisition at 3 T under sedation-induced sleep. Statistical analysis was performed using the timing of spikes, polispikes, modeled with hemodynamic response functions. In patients suffering from LGS, the interictal discharges were associated with positive blood oxygenation level-dependent (BOLD) changes in the brainstem. This was comparable with cortical positive BOLD responses in group II.Moreover, as revealed by group analysis, group I differed from group II according to correlations between BOLD signal and interictal discharges in the brainstem. Conclusions: Using the EEG-fMRI method, it could demonstrate that epileptiform discharges in LGS are associated with hemodynamic changes in the brainstem. The BOLD signal increase in the control group was observed in thalamus, cerebellum and cerebral cortex. It seems likely that the neuronal network complex in the brainstem is responsible for EEG abnormalities in LGS. It has been hypothesized that clinical seizures might result from intermittent interference of descending brainstem pathways controlling spinal reflex activity, whereas activity in the ascending pathways from the same brainstem areas that project wide to the cerebral cortex might produce the characteristic EEG features of LGS. Our results determined that the brainstem is involved in the pathogenesis of LGS.