AbstractApproximately 20–30% of patients with epilepsy continue to have seizures despite carefully monitored treatment with antiepileptic drugs. The mechanisms that underlie why some patients are responsive and others prove resistant to antiepileptic drugs are poorly understood. Increasing evidence supports a role for altered mitochondrial function in the pathogenesis of epilepsy. To gain greater molecular insight in the pathogenesis of intractable epilepsy, we undertook a global analysis of protein expressions in a pharmacoresistant epileptic model selected by phenytoin in electrical amygdala‐kindled rats by using two‐dimensional gel electrophoresis coupled with matrix‐assisted laser desorption/ionization time of flight (MALDI‐TOF‐TOF). We identified five increased proteins and 14 decreased proteins including voltage‐dependent anion channel 1 (VDAC1) with a 2.82‐fold increased level (P < 0.05) and voltage‐dependent anion channel 2 (VDAC2) with a 3.97‐fold decreased level (P < 0.05) in hippocampus of pharmacoresistant rats. The increased VDAC1 and decreased VDAC2 were confirmed by Western blot analysis and immunohistochemistry. Vascular mitochondria and apoptosis neurons were observed through electron microscopy. Energy contents, the adenine nucleotides, were measured by high‐performance liquid chromatography (HPLC). The correlation analyses were carried out between VDAC and the energy charge. These findings indicate that the increase of VDAC1 and the decrease of VDAC2 play an important role during the process and provide new molecular evidence in understanding mechanism of refractory epilepsy. © 2007 Wiley‐Liss, Inc.