We studied two epileptic patients with arachnoid brain cysts by proton magnetic resonance spectroscopy (1H MRS). In addition, histochemical analyses of surgical specimens, cerebrospinal fluid, and cystic fluid were performed in one of the patients. In both patients, greatly increased levels of excitatory amino acids (EAAs) glutamate and aspartate were present in the cystic fluid, while there was only a moderate increase of glutamate in the epileptogenic brain tissue adjacent to the cyst in one of the patients. In non epileptic brain regions, no elevations of the EAAs were present. Since EAAs are involved in induction and maintenance of epileptogenesis, their extremely high concentrations in the cystic fluid may explain seizures in some patients with such brain cysts. Our findings may have therapeutical consequences for patients with drug resistant epilepsy, in whom elevated concentrations of EAAs in the cysts can be verified. Surgery with the aim to create a communication between the cyst and the subarachnoidal space may prevent an accumulation of the EAAs and thus result in a relief of seizures.