To investigate the association between the number of third molars and craniofacial shape. The study sample comprised 470 individuals (194 males and 276 females), out of whom 310 (124 males, mean age: 14.6 years and 186 females, mean age: 14.1 years) had a full permanent dentition including third molars and 160 (70 males, mean age: 13.7 years and 90 females, mean age: 13.9 years) had at least one missing third molar. Pre-orthodontic treatment cephalometric images were digitized using 127 landmarks to describe the shape of the entire craniofacial configuration, the cranial base, the maxilla, and the mandible. The shapes of the various configurations were described by principal components (PCs) of shape. The effect of third molar agenesis on craniofacial shape was evaluated with multivariate regression models, considering shape PCs as the dependent variables, and age and sex as predictors. There was a strong association between third molar agenesis and the shape of all craniofacial configurations in both sexes. Individuals with missing third molars presented a less convex craniofacial configuration, a shorter anterior facial height and a more retrusive maxilla and mandible. In cases with third molar agenesis only in one jaw, shape differences were also evident in the opposing jaw. Interpretation of study outcomes should take into consideration the two-dimensional data and the analysis of only white-European subjects. There is a strong association between third molar formation and craniofacial shape. The effect is rather generalized than local and is potentially linked to an ongoing evolutionary mechanism that leads to smaller and fewer teeth, as well as smaller craniofacial configurations, in modern humans.