Basal cell nevus syndrome (BCNS) is a rare, multisystem, autosomal dominant disorder that is characterized by various phenotypes, including multiple basal cell carcinomas of the skin, odontogenic keratocysts of the jaws, and occasionally cleft lip and/or palate. In this report, we describe a 6-year-old Japanese girl with a novel heterozygous nonsense mutation in PTCH1 who exhibited rare craniofacial phenotypes, such as oligodontia and a short-tooth root.