Septo-optic dysplasia is defined by a variable combination of dysgenesis of midline brain structures including optic nerve hypoplasia and hypothalamic-pituitary dysfunction often associated with a wide variety of brain malformations of cortical development. Multiple congenital anomalies have been reported only sporadically. Despite recent demonstration of the possible pathogenic role of HESX1/Hesx1 gene (a homeobox gene important for development of prosencephalon), the etiology of most cases of septo-optic dysplasia still remains unclear. This report describes eight children (4 males, 4 females; age 2 to 17 years) with septo-optic dysplasia who manifested dysmorphic features (involving not only the midline facial structures) and a spectrum of additional clinical and imaging features including autism, facial hemangioma, and holoprosencephaly. Full mutational screening for the HESX1 gene in seven of eight children was negative. Based on the extreme variability of the clinical and imaging phenotypes hereby observed, on literature review, and on septo-optic dysplasia animal models, this study confirmed that the phenotypic heterogeneity in septo-optic dysplasia is high. We suggest that: (1) dysmorphic features are more frequent than previously thought--they may represent a relevant part of the phenotype; (2) septo-optic dysplasia should be recategorized as an heterogeneous malformation syndrome (septo-optic dysplasia complex) (encompassing multiple brain, endocrine, and systemic anomalies) rather than a single precisely defined entity.