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Reading skeletal morphology in terms of function and so lifestyle is a key aspect of osteological research. While morphometric studies can play a role, an alternative is compare responses to simulated functional loading using Finite elements analysis (FEA). This is usually done using strains but recently the use of Geometric morphometrics to compare the deformations from simulated loading has been proposed. Here we illustrate this approach in a study of the sensitivity of finite element models of the mandible to input variables. These preliminary investigations form part of a study to assess the extent to which human mandibular form and function reflects diet, with direct application to the study of the impact of agriculture on our jaws. In carrying out FEA of the mandible there are many choices to be made with regard to the impact of different methods of constraining it, and different material properties of teeth, periodontal ligament and cancellous bone. Thus, the first step is to consider to what extent the results of FEA reflect reality and the impacts of different modelling decisions. A clinical CT scan is used to build FE models of the mandible with cortical bone, teeth, periodontal ligament and cancellous bone segmented. FEA is carried out using different constraints and material properties. The results are compared using strain maps and geometric morphometrics. How the mandible is constrained has a large effect on the mode and magnitude of mandibular deformation while changing Young’s modulus of teeth, cancellous bone and periodontal ligament to that of cortical bone impacts significantly, but to a lesser degree. The GM analyses show that without detailed and specific validation data there is no certainty that FEA replicates physiological functioning. As such, FEA of the mandible is best applied to questions that do not rely on accurate prediction of physiology.