The authors describe a child who has hypochondroplasia due to an N540K mutation and who has medial temporal lobe dysgenesis. This association has been reported only twice before. FGFR3 is expressed in the brain during development and plays a role in hippocampal formation, and FGFR3 mutations could cause cerebral malformations in hypochondroplasia. Further neuroimaging studies of patients with hypochondroplasia and epilepsy or developmental delay may clarify the proportion of patients with hypochondroplasia with this pattern of central nervous system abnormalities.