A newborn male presented with complete external third nerve palsy of his right eye immediately at birth. Pediatric examination and MRI of the skull revealed no abnormalities. At the age of six weeks, strabismus surgery was performed to facilitate amblyopia treatment. The muscles appeared small and fibrotic. At the age of ten weeks, a brow suspension of the upper lid and a second strabismus surgery were performed. The amblyopia treatment and patching, applied for half of the waking hours over a period of six weeks, were unsuccessful. At the age of six months, a relative pallor of the right optic nerve head became evident. At the age of three years, at a new examination because of growth deficiency, a second MRI revealed defects involving the pituitary region. We concluded that extraocular muscle abnormality or oculomotor nerve palsy was present together with optic nerve dysplasia and pituitary gland malformation.