We report an activating fibroblast growth factor receptor 3 (FGFR3) mutation (R248C) occurring in a verrucous epidermal naevus, and not found in other tissues, in a girl with mild facial dysmorphism. We demonstrate the presence of the mutation in keratinocytes cultured from the naevus and we speculate that a low level of the mutation in other tissues may account for her facial dysmorphism. The possibility that the mutation is present in other tissues implies a possible risk to her future offspring.