Hallerman-Streiff Syndrome is a rare congenital disease characterized by dyscephaly, hypotrichosis,microphthalmia, cataracts, proportionate short stature, skin atrophy, and dental anomalies. Airway management is usually difficult in affected patients, because the dyscephaly in this syndrome includes micrognathia and microstomia. We treated a 13-day-old male with Hallerman-Streiff Syndrome who was presented with a natal tooth in the anterior region of the upper jaw. The natal tooth was apparently unstable because of a small tumor-like lesion in the gingiva and X-ray images revealed no root formation. In addition, micrognathia, microstomia, and thoracocyllosis were found in association with Hallerman-Streiff Syndrome. These findings raised the possibility that the natal tooth might easily become dislodged, and then be difficult to find and remove from the oral cavity. Under local anesthesia we excised the tumorous gingiva along with the natal tooth and occluded the bleeding point with an absorbable suture. The postoperative course was satisfactory. Herein, we discuss risks and treatment of a natal tooth in patients with craniofacial anomalies, particularly micrognathia and microstomia.