To compare craniofacial and cervical morphology between skeletal Classes II and III applying Geometric Morphometric Methods (GMM). Twenty-six cervical and craniofacial landmarks of 40 Class II and 39 Class III individuals were digitalized on lateral cephalograms. Procrustes ANOVA, generalized Procrustes, principal component analyses, and thin-plate spline function were applied to assess the pattern of shape variation of craniofacial structure and the cervical spine in relation to skeletal classes. Compared with Class III, Class II individuals presented a maxillary protrusion, mandibular retrusion, shorter mandibular corpus, posterior mandibular ramus rotation, anterior cranial base rotation, and a smaller centroid size. Furthermore, a forward and smaller cervical spine were observed. With GMM, the shape and size differences between skeletal classes can be analyzed visually and numerically.