The purpose of this study was to determine whether the morphology of the midface differed in normal (Class I) and midfacially-retrognathic (Class III) prepubertal subjects, and to localize differences morphometrically. Lateral cephalographs of 133 European-American children between 5-11 years of age were traced and average geometries, scaled to an equivalent size, were generated based upon seven nodes (pterygoid point, PTS; rhinion, RO; posterior nasal spine, PNS; midpalatal point, MPP; anterior nasal spine, ANS; subspinale, A; and prosthion, Pr). The samples also were subdivided into seven age- and sex-matched groups for morphometric comparisons. Procrustes analysis indicated that the overall midfacial configurations differed statistically (P < 0.05). Therefore, a color-coded finite element (FEM) program was used to localize differences in morphology graphically. Comparing Class I and III groups for size-change, FEM revealed that negative allometry was evident in the posterior half of the midfacial configuration localized between PTS, PNS, and MPP. The anterior half was more isotropic, however, but the anterior-most aspect of the configuration between Pr and RO showed some positive allometry particularly in the premaxillary and incisor regions. For shape-change, major differences in shape over the entire midface were not as evident, with an isotropic midfacial morphology for normal and Class III subjects. It is concluded that an identifiable pattern of deformation is evident for the Class III subjects during the prepubertal growth period. Therefore, midfacial retrognathia associated with Class III malocclusions results, at least in part, from deficient anteroposterior elongation of the midfacial complex allied with deformation of the premaxillary region.