SOX-3 is a transcription factor expressed throughout the developing central nervous system and is involved in maintenance of pluripotency in self-renewing stem cells, specification events, lineage progression, and terminal differentiation. An association between growth hormone deficiency, mental retardation, and Sox-3 mutations in humans was previously reported. The occurrence of abnormalities affecting the polyalanine tract of the Sox-3 gene was determined in a group of 77 unrelated mentally retarded patients without a definite genetic diagnosis and in 84 control subjects. A new SOX-3 polyalanine tract deletion was identified in a mentally impaired boy, in his mother (homozygous), and in 2 healthy brothers of the proband. This new mutation does not segregate with mental retardation.