Focal cortical dysplasia (FCD) is a rare, sporadic disorder which is a recognised cause of chronic epilepsy. It is proposed to result from disordered neuronal migration and differentiation and has characteristic histological features which include disturbed cortical lamination, large abnormal neurons and the presence of large balloon cells with glassy eosinophilic cytoplasm and pleomorphic eccentric nuclei. These latter express both glial and neuronal markers indicative of abnormal neuroglial differentiation. In this paper we review the current literature on the neuropathology of FCD and discuss potential mechanisms. We focus on growth factors, signalling pathways and candidate genes with known roles in Drosophila and vertebrate brain development that could be responsible for the developmental brain changes seen in FCD. At issue are the factors that influence cell fate and differentiation and which regulate neural migration. Some of the molecular pathways, such as those involving the Notch and the Wnt pathways have particularly important roles in neuroglial differentiation in vertebrates, and these are proposed as potential candidates.