Two children are described who presented with fever and generalized seizures, days 50 and 200, respectively, after matched unrelated donor-bone marrow transplantation. Upon antiepileptic treatment the seizures vanished but somnolence and fever remained. Magnetic resonance imaging (MRI) of the brain was performed and revealed transient asymmetric multifocal hyperintense lesions. Seizures were considered related to infection, and the cyclosporin A (CsA) treatment was not interrupted. Enterovirus was detected by reverse transcriptase-polymerase chain reaction in the spinal fluid of one patient and in the sputum of the other. Both children recovered completely within the next weeks without neurological sequel. This report shows that enteroviral meningoencephalitis can present with seizures during the post-transplant period. It highlights the importance of MRI for neuroimaging and of viral infections as differential diagnosis to CsA neurotoxicity.