Fraser syndrome (FS) is a rare recessive autosomal genetic disorder characterized by multisystemic malformations typically comprising cryptophthalmos, syndactyly, and renal defects. We report the case of a 16-year-old patient who exhibited facial asymmetry, short roots, hypodontia, and malocclusion. Oral rehabilitation included orthodontics, exodontia, and osseointegrated dental implants to improve the patient's self-esteem and eating function. We suggest short roots and hypodontia assessment in patients with FS.