The study aimed to evaluate differences in tooth size between patients with hypodontia and those with normal complement of permanent teeth using three-dimensional geometric morphometric analysis. The number of anatomical landmarks was recorded on the clinical crown of the permanent teeth on three-dimensional scanned study models of hypodontia and in control subjects. The study sample comprised 120 patients with hypodontia (mild, moderate, severe) and 40 controls matched for age and sex. Tooth size differences were tested statistically using multivariate statistics. Size variation was for the most part found to be significant, especially when the control subjects were compared with the hypodontia groups. The explained variance among group membership was generally larger in the anterior and premolar region than in the molar region Sexual dimorphism was found less in the anterior region than in the posterior region; therefore, the sexes were pooled more often for teeth in the anterior region. Quantitative measurement of tooth size in patients with hypodontia may enhance the multidisciplinary management of these patients.