Children with Apert syndrome seem to have big eyes. In fact, the eyeballs are a normal size. The problem is that the bones surrounding the eyes (the orbits) cannot grow forward in a normal way. In addition, the eyelid openings usually slant downwards. Some children's eyes can "bulge" so far forward (this condition is called proptosis, or exophthalmos) that the cornea of the eye can become exposed. Occasionally, when children with severe proptosis cry, their eyelids can get temporarily caught behind the eyeball. This condition obviously requires immediate treatment either with a tarsorrhaphy (sewing the outside part of the upper and lower eyelids together) or by surgically moving the bones of the orbits forward (this is usually done at the same time that the forehead is brought forward). Some children with Apert syndrome may also develop optic nerve atrophy (weakening, or wasting), which can diminish a child's ability to see. It is not clear what causes this optic nerve atrophy, but it may be related to chronically elevated intracranial pressure.

The eye problem most frequently found is an imbalance of the muscles that move the eye (called "strabismus"). Sometimes, one of the six muscles that move the eye may be completely absent. Many children with Apert syndrome require eye muscle balancing surgery. If this is not done, children learn to stop seeing out of one eye ("amblyopia") in order to prevent seeing double images.

The mid face is the part of the face that extends from underneath the eyes and across the top of the nose, down to the teeth of the upper jaw. This area is always small (also called "hypoplastic", meaning lack of growth) in Apert syndrome. The deepest part of the face is usually centered at the top of a short nose. Because the mid face cannot grow forward very well, it is usually surgically moved forward a couple of times over the child's lifetime (see the treatment section). From measurements taken from our center in Dallas, it appears that the face in children with Apert syndrome grows only about 1/3 normal speed, and there is additional evidence to suggest that all forward growth stops about age 9 (see publications [ #24, 2005]).