Individuals with congenitally missing permanent teeth, other than third molars, present smaller craniofacial configurations compared to normal controls. However, it is not known if agenesis of third molars is part of the same mechanism. Therefore, this study assessed individuals with and without isolated third molar agenesis and tested the relation of this condition to the size of their facial configurations, using geometric morphometric methods. We show that the absence of one or more third molars is associated with a smaller maxilla, smaller mandible and a smaller overall facial configuration. The effect was larger as the number of missing third molars increased. For example, the size of the mandibular centroids in five 16-year-old females with no, one, two, three or four missing third molars showed a size reduction of approximately 2.5 mm per missing third molar. In addition, in cases with third molar agenesis in one jaw only, the effect was also evident on the opposite jaw. Our findings suggest that isolated third molar agenesis is part of a developmental mechanism resulting also in craniofacial size reduction. This might be the effect of an evolutionary process observed in humans, leading to fewer and smaller teeth, as well as smaller facial structures.