Objective To identify certain craniofacial characteristics of untreated prepubescence Class II patients with deep and shallow mandibular notching. Methods 18 untreated preadolescent Class II patients with deep mandibular notching and 17 untreated preadolescent Class II patients with shallow mandibular notching were selected. Each subject's pretreatment lateral cephalogram was traced. Seventeen angular and eleven linear measurements were made. The means and standard deviations were calculated for each parameter. The significance of difference between mean values was evaluated by the Independent-Samples T test. Differences were considered statistically significant when the P value was 0.05 or less. Results There was no difference in ANB between two groups, but deep notch cases had more retrusive maxillary and mandibles with shorter maxillary and corpus. In vertical direction, subjects with a deep mandibular notch had a longer lower facial height and more vertically directed mandibular plane angle than did shallow notch cases, these may be caused by the increasing of alveolar height of maxillary, smaller ramus height and greater gonial angle. Conclusion There were some differences in the craniofacial morphologies between deep and shallow notching groups of preadolescent Class II patients. Compared with shallow notching group, the mandibles with the deep notching rotated downward and backward and have more vertical directed tendency, but there have no obviously difference in horizontal relationship of maxillary and mandible between two groups.