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In view of concerns relating to the validity of traditional cephalometric appraisals, we undertook this study to use a potentially powerful method, finite element analysis, to compare cephalometric changes between two samples (subjects with and without orthodontic treatment). The derived data show varying sample contrasts depending on the particular finite element array included in the analysis. Thus, although finite element analysis facilitates rigorous morphometric analysis, further investigation is required before it can be applied universally in cephalometric studies.