We report a rare case of an embedded supernumerary tooth in the left pterygoid process region of a patient with first and second branchial syndrome. A 3-month-old Japanese boy was referred to our clinic for treatment of a lateral facial cleft. The patient, birth weight 2960g, was born to a 29-year-old mother following an uncomplicated full-term pregnancy. He had a left lateral facial cleft, a left lateral cleft palate, a midline mandibular cleft, and absence of the left coronoid process. The surgical procedures were directed at repairing the anatomic defects of the left lateral facial cleft and the lower lip cleft at the age of 5 months. Then, a block iliac bone was used to repair the median cleft at the age of 6 years 2 months. In a panoramic radiograph at 2 years 8 months of age, an embedded supernumerary tooth was recognized near the left pterygoid process. We regularly observed the supernumerary tooth on panoramic radiographs until he was 21 years old. We have no reliable information on its origin because there is no cleft at the upper alveolar arch of the maxilla of this patient. Perhaps the supernumerary tooth originated from the dental germ in the coronoid process and wandered into the pterygoid process because of the