We report a rare case of growth hormone and gonadotropin deficiency associated with dysmorphic features. A 16-year-old boy had left anophthalmia, microphallus, bilateral cryptorchidism, and mental retardation. His chromosomal karyotype was normal, 46, XY. Endocrinological studies revealed growth hormone and gonadotropin deficiency, attributed to hypothalamic dysfunction. Magnetic resonance imaging scan of the head showed a hypoplastic pituitary gland, decreased high intensity signals in the pituitary posterior lobe, absence of the left eye, and a hypoplastic left optic nerve with no abnormality of the pituitary stalk, corpus callosum, or septum pellucidum. Although not completely consistent with the features of septo-optic dysplasia (SOD), his condition was considered within the spectrum of SOD. Despite similarities to the Hesx1 knockout mouse, a model of human SOD, mutation analyses revealed no mutations or polymorphisms in coding regions of any exons or intron-exon boundaries of the HESX1 gene. Further genetic studies of this patient may improve understanding of molecular mechanisms involved in pituitary development.