We describe three patients with benign partial epilepsy with centrotemporal spikes (BECT) in association with proven brain lesion (agenesis of the corpus callosum, lipoma of the corpus callosum, and congenital toxoplasmosis, respectively). The age of onset, the ictal signs, the interictal electroencephalographic findings and the favorable outcome of epilepsy even after withdrawal of drug therapy led to the diagnosis of BECT although organic brain lesions were present. In such cases, the epilepsy should not be ascribed to the lesions but should be considered benign even though fortuitiously associated with brain lesions.