Background: To study the covariation between palatal and craniofacial skeletal morphology in Class III growing patients through geometric morphometric analysis (GMM). Methods: In this retrospective study, 54 Class III subjects (24F,30M;7.6±0.8yy) were enrolled following these inclusion criteria: European ancestry, Class III skeletal and dental relationship, early mixed dentition, prepubertal skeletal maturation, familiarity for Class III malocclusion, no pseudo Class III malocclusion. Each patient provided upper digital cast and cephalogram before starting the therapy. Landmarks and semilandmarks were digitized (239 on the casts;121 on the lateral radiographs) and GMM was used. Procrustes analysis and principal component analysis (PCA) were applied to show the principal components of palatal and craniofacial skeletal shape variation. Two-block partial least squares analysis (PLS) was used to assess pattern of covariation between palatal and craniofacial morphology. Results: Regarding palatal shape variation, PC with largest variance (PC1) described morphological changes in the three space dimensions, while, concerning the craniofacial complex components, PC1 revealed morphological differences along the vertical plane. A significant covariation was found between palatal and craniofacial shape. PLS1 accounted for more than 61,7% of the whole covariation, correlating the craniofacial divergence to palatal height and width. Conclusions: In Class III subjects increments of angle divergence are related to a narrow and high palate.