Perhaps the single most identifying feature of Apert syndrome is the syndactylies, or fusion, of all the fingers and toes. During normal development, when a baby is growing inside of his or her mother, all the fingers and toes begin their growth completely fused together. At some point in development, a signal is sent to the hands and feet, which results in all the fingers and toes separating. This process is does not occur in Apert syndrome, so that this normal separation of the fingers and toes either does not occur, or occurs just between the thumb and index finger (and rarely between the ring and small fingers).

Apert syndactylies are classified according to how many fingers are fused together (Types I-III). In the mildest cases, only the index, long and ring fingers are fused, and each has it's own nail. In the more severe cases, all the fingers are fused together (often referred to as a "rosebud hand"). Occasionally, the thumb is completely buried underneath the skin of the palm. Typically, the bones of the thumb grow slanted instead of straight, so that the tip of the thumb curves away from the index finger. When the bones of the fingers are fused together, they are always fused near the tips under the nails (the nail plates are usually fused together, as well). In addition, the index, long, ring and small fingers are all missing the middle joint (called the PIP, or proximal interphalangeal joint).

The toes almost always have completely separate nails. Bony fusion between the toes is very rare, and when it does occur, it is usually only between a couple of the toes. The big toes are shorter than normal, and frequently grow like the thumbs, curving away from the rest of the foot. Often the small toes will curve away from the foot as well, fanning out all the toes. This widening of the foot makes it difficult to fit shoes properly, and families usually end up buying shoes a size too large to accommodate the width. Actually, the Apert foot is much shorter than normal and the width is either normal or slightly increased. Three "bumps" may grow on the Apert foot. The first is along the inside of the foot, just behind the big toe. The second is along the outside of the foot, just behind the small toe. The third is on the bottom of the foot, in line with the second toe. The treatment of these bumps, and the syndactylies is discussed in the Treatment section.

Below are representatives of the three types of syndactylies, the degree of attachment of the thumb: completely free, attached by skin, or attached by skin and bone, help determine the type. Five-fingered hands can be routinely obtained from all three types.

Type I

Type II

Type III