The Val66Met polymorphism in the brain-derived neurotrophic factor (BDNF) gene may modulate the epilepsy phenotype. We investigated the impact of polymorphisms in the BDNF gene on clinical features in fragile X syndrome (FXS). In our study sample, the Met66 allele associated with epilepsy of finnish FXS men. Abnormalities in BDNF-mediated plasticity are shown in FXS and the present data suggest that the Met66 allele might predispose FXS males to epilepsy.