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The purpose of this study is to suggest a patient-specific osteotomy line to optimize the distractor position and thus to minimize the disadvantages of conventional mandibular distraction osteogenesis (MDO) protocols. In addition, this study also aims to compare the conventional MDO protocols with the new MDO protocol proposed in this study in terms of both orthodontic outcomes and mechanical effects of osteotomy level on callus stabilization by means of the finite element method.A preoperative patient-specific 3-dimensional bone model was created and segmented by using computed tomography images of an individual patient. Virtual orthodontic set-up was applied to the segmented model prior to the virtual surgery. In order to compare the proposed osteotomy line with the conventional lines used in clinical applications, virtual surgery simulations were performed and callus tissues were modelled for each scenario. The comparison of the success of each osteotomy line was carried out based on the occlusion of the teeth.The osteotomy line determined using the method proposed in this study has resulted in far less malocclusion than the conventional method. Namely, any angular deviation from the optimum osteotomy line determined in this study might result in deep-bite or open-bite. On the other hand, the finite element analysis results have indicated that this deviation also negatively affects the callus stability.In order to achieve a better MDO treatment in terms of occlusion of the teeth and the callus stability, the location of the osteotomy line and the distractor position can be computationally determined. The results suggest that MDO protocol developed in this study might be used in clinic to achieve a better outcome from the MDO treatment.