An 8 -month-old girl was examined because of corneal clouding and microphthalmos. The fundi of both eyes could not be visualized because of corneal clouding. Orbital and cranial computerized tomographic scanning and magnetic resonance imaging demonstrated bilateral microphthalmos and presumed retinal dysplasia, hypoplasia of the optic nerves and chiasm, agenesis of the septum pellucidum, thinning of corpus callosum, and a normal pituitary infundibulum. Cerebral cortex and white matter were unremarkable. Other ocular malformations were anterior segment dysgenesis in the right eye and congenital cataract or lens abnormality in the left eye. Endocrine studies revealed normal serum hormone levels. There were no colobomatous lesions and systemic anomalies suggestive of a coloboma syndrome. This case represents the rare association of septo-optic dysplasia with complex microphthalmos.