The pathophysiology of combined pituitary hormone deficiency is just beginning to be elucidated. None of the genes known to be necessary for pituitary development has so far been involved in pituitary gland aplasia in humans. Among these, Hesx1/HESX1, which encodes a homeobox transcription factor, has been shown to be essential for normal forebrain development in mice, and HESX1 mutations in humans have been associated with various pituitary hormone deficiencies usually combined with optic nerve anomalies. Here we have investigated a consanguineous family in which two siblings displayed a complete absence of the anterior pituitary revealed by a deficit in all anterior pituitary hormones. One patient, who also has retinal coloboma, carries a HESX1 defect in the homozygous state: an Alu insertion in exon 3, a sequence that encodes the major part of the homeodomain. The Alu-containing HESX1 allele generates a major transcript lacking this exon, and a minor one in which exons 2 and 3 are skipped, predicting severely truncated proteins. This observation, which combines pituitary aplasia and retinal coloboma, further illustrates the heterogeneity of HESX1-associated disease phenotypes. Anterior pituitary aplasia is a new example of a human disease caused by a germline retrotransposition event involving an Alu sequence. © 2005 Wiley-Liss, Inc.