Context: Heterozygous, de novo mutations in the transcription factor SOX2 are associated with bilateral anophthalmia or severe microphthalmia and hypopituitarism. Variable additional abnormalities include defects of the corpus callosum and hippocampus.Objective: We have ascertained a further three patients with severe eye defects and pituitary abnormalities who were screened for mutations in SOX2. To provide further evidence of a direct role for SOX2 in hypothalamo-pituitary development we have studied the expression of the gene in human embryonic tissues.Results: All three patients harboured heterozygous SOX2 mutations; a deletion encompassing the entire gene, an intragenic deletion (c.70_89del), and a novel nonsense mutation (p.Q61X) within the DNA binding domain that results in impaired transactivation. We also show that human SOX2 can inhibit -catenin-driven reporter gene expression in vitro, whereas mutant SOX2 proteins are unable to efficiently repress this activity. Furthermore, we show that SOX2 is expressed throughout the human brain including the developing hypothalamus as well as Rathke's pouch, the developing anterior pituitary and the eye.Conclusions: Patients with SOX2 mutations often manifest the unusual phenotype of hypogonadotropic hypogonadism, with sparing of other pituitary hormones despite anterior pituitary hypoplasia. SOX2 expression patterns in human embryonic development support a direct involvement of the protein during development of tissues affected in these individuals. Given the critical role of Wnt-signalling in the development of most of these tissues, our data suggest that a failure to repress the Wnt--catenin pathway could be one of the underlying pathogenic mechanisms associated with loss-of-function mutations in SOX2.