In this work, we present a method to estimate the pose of teeth in pathological dental models. For each tooth of a pathological model, we aim at computing its orientation and position with respect to a healthy dentition. The proposed method is based on the registration of a reference model on a patient-specific 3D segmented mesh. Dental features, such as the arch forms and their types, are derived. These features, combined with registration information, allow our system to propose a plausible target dental arrangement and thus estimate the pose of each tooth. The key contributions of this work are (a) the use of a registered reference model to derive dental features and quantify orthodontic disorders and (b) the automatic estimation of a target dental arrangement.