Cleidocranial dysplasia (CCD) is a congenital anomaly characterized by the presence of impacted supernumerary teeth and delayed eruption of permanent teeth. However, there has been no detailed investigation on supernumerary teeth in patients with CCD using three-dimensional (3D) imaging techniques. The purpose of this study was to elucidate the morphology and position of supernumerary teeth using 3D images reconstructed from cone-beam computed tomography (CBCT) data in a group of five Japanese subjects (male, 3; female, 2; age, 15.0-25.4 years) with CCD. All five subjects exhibited supernumerary teeth (39 in total; average, 7.8; range, 1-15). All supernumerary teeth were impacted and existed as pairs with adjacent permanent teeth. Comparison of the size (the crown and dental-root lengths, the crown mesiodistal and buccolingual diameters), the number of cusps and dental roots, the position, and direction of supernumerary teeth in relation to the adjacent permanent teeth was analyzed. The results of relationship analyses revealed that, at sites other than the molar region, supernumerary teeth were positioned on the lingual and distal sides and supernumerary teeth resembled the morphology of their adjacent permanent teeth in terms of the number of cusps but were smaller than the adjacent permanent teeth. In the molar region, supernumerary teeth were microdontia, which were apparently small and obscure morphologically. In addition, while all adjacent permanent teeth exhibited normal direction, five supernumerary teeth exhibited inverse direction. The findings of this study will improve our understanding of the characteristics of CCD and provide important information for the pathophysiology and clinical treatment.