This study was designed to examine the relationship between third molar agenesis and skeletal morphology in the Chinese population. A total of 1043 patients' records were analyzed with panoramic radiographs and cephalograms. Congenitally missing third molars were assessed with respect to gender, jaw, and side, and assessed in various types of facial morphology. Linear, angular, and proportional cephalometric measurements were analyzed and compared among the samples. For the evaluation of results, the following statistics were used: the Pearson chi (2) test, one-way ANOVA, and the Student-Newman-Keuls method. The overall prevalence of third molar agenesis was 28.7%. Missing third molars were more common in the maxilla and on the right side, while the difference was not statistically significant (P > 0.05) between genders. Every hypodontia group had a smaller SN-GoGn angle, Y-axis-FH angle, and a larger S-Go/N-Me ratio. The group with third molar agenesis in both jaws had smaller SNA and Wits values. The frequency of third molar agenesis in subjects with a Class II malocclusion was significantly lower than in other types of malocclusion (P < 0.05), and the incidence of third molar agenesis in hypodivergent growth pattern was higher than in other patterns (P < 0.05). The results demonstrate a possible association between third molar agenesis and both sagittal and vertical craniofacial morphology.