Malformations of cortical development (MCDs) are increasingly being recognized as a common cause of epilepsy in cases previously felt to be cryptogenic. MCDs occur when the normal process of cerebral cortical development is disrupted, and include disorders of neuronal proliferation, migration, and organization. Many have a genetic basis and the genes responsible for some MCDs have been identified. MCDs represent a unique and valuable substrate in functional brain mapping studies, since as developmental lesions they provide complementary information to studies performed on patients with acquired brain lesions. In recent years an increasing number of functional neuroimaging methods, including positron emission tomography, single photon emission computed tomography, magnetic resonance spectroscopy, and functional magnetic resonance imaging, have been applied to patients with MCDs. In this review we highlight some of the prominent findings in this emerging field by presenting the functional neuroimaging characteristics of selected MCDs.