Axenfeld-Rieger syndrome is a rare autosomal dominant disorder characterized by various ocular and extraocular malformations. The incidence of Axenfeld-Rieger syndrome has been estimated to be 1 per 200,000. The syndrome is characterized by short body stature, delayed bone age, and deficient or arrested development of neural crest cells involving the anterior chamber of the eyes, facial bones, teeth, periumbilical skin, and cardiovascular system. This is a case of a 6 year-old girl, who came to the department of the pediatric dentistry, Yonsei University Dental Hospital, for evaluation and treatment of multiple congenital missing permanent teeth. The patient presented typical dental, craniofacial, and systemic features of Axenfeld-Rieger syndrome, such as glaucoma, oval pupil, heterochromatic iris, umbilical hernia, and delayed bone age. On the panoramic view, 3 primary teeth were missing and 13 permanent tooth germs were absent. On the lateral cephalograph, underdevelopment of the maxilla and normal growth pattern of the mandible were confirmed. Periodic dental follow-up is planned for evaluation and interceptive treatment of her dental and craniofacial problems. Denture or removable space maintainer with a pontic is considered for esthetic and functional restoration. In addition, orthognathic surgery is also planned in future to prevent further midfacial skeletal deformation. Early diagnosis of Axenfeld-Rieger syndrome is very important to prevent exacerbation of complications, such as glaucoma and skeletal deformities.