A prospective neurological and electroencephalographic (EEG) study was performed in sixteen leukemia patients receiving busulfan (BU) and cyclophosphamide before autologous bone marrow transplantation. All patients were given anticonvulsant prophylaxis with a combination of phenobarbital (PB) and clonazepam (CLZ). Neurological examination and EEG were performed prior to and soon after completion of BU treatment and were repeated two months later. No tonic-clonic and/or myoclonic convulsions were observed. In two patients, comparison of EEG recorded before and upon completion of BU administration revealed modification of features. EEG re-evaluated two months after BU showed normalization in one of the two patients. BU may trigger both generalized and myoclonic seizures together with EEG abnormalities; PB combined with CLZ may be useful prophylactic treatment.