The aim of this study was to evaluate changes in shape of the palatal vault after maxillary expansion with hyrax expander (HE) and leaf expander (LE), using 3D Geometric Morphometric Analysis. Overall, 250 patients (110 M, 140 F) with maxillary transverse deficiency were selected for this study. In this study, 127 subjects were treated with HE, 123 with LE. Digital dental models were obtained pre-treatment (T0) and after 12 months from the cementation of the device (T1) and processed by means of a digital scanner. Linear and morphometric analyses were conducted to determine the effects of each appliance on dental measurements and palatal shape, and a multiple linear regression was performed to analyse the influence of anchorage and appliance type on final shape. Morphometric analysis showed that there was a lowering of the palatal vault in the HE group, while in the LE group it remained unchanged: the difference in palatal shape at time T0 and T1 was statistically significant in both treatments (HE vs. LE). In the HE group, the change in shape also included the upper part of the palatal vault in the vertical dimension, while in the LE group the change in shape interested mainly palatal shelves and the lower portion of the palate. Both LE and HE produce clinically significant changes in the morphology of the palatal vault.