Cortical dysgenesia are a heterogenous group of genetic or acquired disturbances of cortical development which, due to the enormous progress in modern neuroimaging techniques, are increasingly recognized in association with a variety of clinical disorders. The spectrum of clinical manifestations, depending on type and extent of the alterations, includes severe mental retardation and epilepsy as well as neuropsychological deficits and some psychiatric disorders. Although pathogenesis and pathophysiology of cortical dysgenesis are still not fully understood, the recent discovery of responsible genes, growth factors, neurotransmitters, and exogenous factors sheds light on elementary mechanisms. The development of animal models mimicking different types of human cortical malformations helped to increase further the understanding of functional consequences of focal cortical dysgenesis. Several studies on these models reveal widespread alterations of cortical connectivity and excitability which are probably of crucial importance in different clinical disorders.