Isolated GH deficiency or combined pituitary hormone deficiencies have been associated with mutations in transcription factors encoding genes that control organogenesis or cell differentiation. Among these factors, Hesx1 is essential for the development of the optic nerve and regulates some of the earliest stages in pituitary development and is intimately involved in orchestrating the expression of other factors involved in pituitary organogenesis. Mutations in HESX1 are reported in patients with hypopituitarism either with typical septo-optic dysplasia (SOD) or with neuromorphological abnormalities not included in classical SOD. The present report describes clinical features, biochemical parameters, and characterization of a missense mutation (Gln6His) in exon1 of HESX1 in a pre-pubertal child who progressively developed multiple hypopituitarism, firstly GH and, afterwards, TSH and ACTH deficiencies, in a pluri-malformative syndrome characterized by short stature and anatomical malformations not associated with a classical SOD phenotype. This finding further supports the necessity to stay alert in evaluating a gene that plays a minor role in the pathogenesis of sporadic hypopituitarism, such as HESX1 gene even when the phenotype does not fit in with a classical SOD syndrome.