Background and objective: Agenesis of the maxillary lateral incisor occurs in up to 4% of all individuals and requires multidisciplinary treatment. Its developmental origins, however, are not fully understood. Earlier studies documented genetic factors contributing to agenesis but also an association with craniofacial morphology. In this study, we assessed the association between maxillary morphology and lateral incisor agenesis by a geometric morphometric approach to disentangle the roles of developmental plasticity and genetic factors. Materials and methods: We quantified the maxillary alveolar ridge by 19 two-dimensional landmarks on cross-sectional images of 101 computed tomography scans. We compared the shape and size of the alveolar ridge across patients with unilateral or bilateral agenesis of maxillary lateral incisors and patients with extracted or in situ incisors. Results: The maxillary alveolar ridge was clearly narrower in patients with agenesis or an extracted incisor compared to the control group, whereas the contralateral side of the unilateral agenesis had an intermediate width. Despite massive individual variation, the ventral curvature of the alveolar ridge was, on average, more pronounced in the bilateral agenesis group compared to unilateral agenesis and tooth extraction. Conclusions: This suggests that pleiotropic genetic and epigenetic factors influence both tooth development and cranial growth, but an inappropriately sized or shaped alveolar process may also inhibit normal formation or development of the tooth bud, thus leading to dental agenesis. Clinical relevance: Our results indicate that bilateral agenesis of the lateral incisor tends to be associated with a higher need of bone augmentation prior to implant placement than unilateral agenesis.