Variation in masticatory induced stress, caused by shape changes in the human skull, is quantified in this article. A comparison on masticatory induced stress is presented subject to a variation in human skull shape. Non-rigid registration is employed to obtain appropriate computational domain representations. This procedure allows the isolation of shape from other variations that could affect the results. An added benefit, revealed through the use of non-rigid registration to acquire appropriate domain representation, is the possibility of direct and objective comparison and manipulation. The effect of mapping uncertainty on the direct comparison is also quantified. As shown in this study, exact difference values are not necessarily obtained, but a non-rigid map between subject shapes and numerical results gives an objective indication on the location of differences.