Mutations in the Methyl-CpG-binding protein 2 (MECP2) gene have been implicated in the etiology of Rett syndrome (RTT), a neurodevelopmental disorder that primarily affects girls. MECP2 mutations in males, once thought to be lethal, are now recognized with a broad spectrum of clinical manifestations. Here we report a 3-year-old boy who presented with developmental problems and regression and eventually was diagnosed with RTT that genetic analysis revealed to be a hemizygous c.316C>T missense mutation in the MECP2 gene suggesting somatic mosaicism with the normal 46,XY karyotype. DNA analysis of the patient's mother showed this either to be a de novo mutation or a case of gonadal mosaicism. To the best of our knowledge, this is the first case report of RTT in a young boy with a hemizygous c.316C>T mutation in the MECP2 gene.