Apert syndrome is a clinically heterogeneous skeletal disorder with features overlapping those of Crouzon, Pfeiffer, and Jackson-Weiss acrocephalopolysyndactyly syndromes, with which it is allelic. There is considerable variation in clinical severity, with some patients so mildly affected that they appear almost normal, while others have more severe facial deformities, and still others have syndactyly, sometimes to a marked degree. Pre- and postaxial polydactyly may be present. Progressive synostosis occurs in hands, cervical vertebrae, carpus, tarsus, and of course in the skull, which leads to acrocephaly. The midface is usually flattened.

A small but significant number of individuals have developmental delay and cognitive impairments.