Thanatophoric dysplasia (TD) is a relatively common, fatal form of chondrodysplastic dwarfism in which the cerebral cortex displays a unique and complex malformation. The malformation is characterized by a combination of abnormalities, which affect the temporal lobe most severely. Salient features include temporal lobe enlargement, deep transverse sulci across the inferomedial temporal surface, and hippocampal dysplasia. TD is caused by mutations of the fibroblast growth factor (FGF) receptor 3 gene (FGFR3), which result in constitutive activation of the FGFR3 tyrosine kinase. However, the link between constitutive FGFR3 activation and malformation of the cortex has been difficult to elucidate. In this review, I describe the neuropathological features of human TD, especially the cortical malformation, ascertained by examination of 45 published cases and 5 new cases, spanning gestational ages from 18 to 42 weeks. The cortical malformation is interpreted with regard to developmental mechanisms, and observations from a mouse model of TD. The evidence suggests that FGFR3 activation perturbs three key processes in cortical development: areal patterning, progenitor proliferation, and apoptosis. Defective patterning accounts for hippocampal dysplasia, while increased proliferation and decreased apoptosis account for temporal lobe hyperplasia and premature development of aberrant sulci. Disturbances in these processes may also contribute to other cortical malformations.