Background and Objectives: Ectodermal dysplasia (ED)—a genetic disorder—is characterized by severe tooth deficiency. We compared the mandibular volume and the sagittal and horizontal mandibular widths between patients with ED (ED group) and individuals without tooth deficiency (control group) using three-dimensional modeling. We hypothesized that the mandibular volume differs in ED cases owing to congenital tooth deficiency. Materials and Methods: We used previously obtained cone-beam computed tomography (CBCT) images of 13 patients with ED. The control group data comprised retrospective CBCT images of patients of similar age and sex with a skeletal relationship of class 1. Further, using the three-dimensional image analysis software, the tooth crowns were separated from the mandible, the mandible was reconstructed and the gonion-to-gonion distance in the mandible was marked, the distance to the menton point was measured, and the distance between the two condyles was measured and compared with the control group. Results: Overall, 46.2% and 53.8% of the participants were men and women, respectively. In the ED group, the mean age of the participants was 15.46 (range, 6–24) years, and the mean number of mandibular teeth was 4.62. Notably, the edentulous mandible volume of the ED group (27.020 mm3) was statistically significantly smaller than that of the control group (49.213 mm3) (p < 0.001). There was no difference between the two groups in terms of the marked points. For data analysis, the Shapiro–Wilk test, independent samples t-test, and Mann–Whitney U test were used. Conclusions: It has been considered that mandible volume does not develop in ED cases because of missing teeth. Modern practices, such as the CBCT technique and three-dimensional software, may be effective in identifying the true morphologic features, especially in patients with genetic syndromes affecting the maxillofacial structure.