Development of the human facial structures including the jaws and dentition occurs in a process that has the characteristics of a complex adaptive system (CAS) influenced by epigenetic, genetic and environmental factors. Earlier studies have suggested dental arch development to be reduced in size in subjects with hypodontia when compared with controls. Hypodontia is a variation of development and presents with a reduced number of teeth together with several other phenotypic changes. This study uses enhanced 3D imaging techniques to increase the accuracy of the measurements of dental arches. The sample consists of orthodontic patients, 60 with hypodontia (thirty males and thirty females), and 60 controls matched for age, gender and ethnicity. One operator using an Amann Girrbach Ceramill Map400 3D scanner recorded the 3D images from dental models. The 3D images were then viewed on MeshLab and the accuracy of the measurements were determined through repeat measurement of the same images; this was undertaken with intra-and inter-operator reproducibility. Ten repeat measurements were taken on 10 different models. Validation of the new system was undertaken by repeating the measurements using the standard 2D caliper technique. Arch dimension measurements were determined from distance between the left-hand side first molar to the right-hand side first molar. Similar measurements were also made for the inter-canine width. The results for average intraoperator measurements were 0.33 mm for the maxillary arch and 0.40 mm for the mandibular arch. The difference in average inter-operator reproducibility was also measured for inter-molar arch dimensions at 0.31 and 0.23 mm for maxillary and mandibular arches, respectively. This novel method provides an increased range of measurement of similar accuracy to standard techniques. This study will proceed to establish the variations on the 3D images between the hypodontia subjects and the control group.