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Automatic identification of the Frankfurt plane (FP) and mid-sagittal plane (MSP) of a human skull is a very important task. These planes are used to define important landmarks on the skull for surgery planning and guidance, forensic reconstruction, and anthropological and archaeological studies. At present, there is no known method for automatic identification of FP. Existing methods identify FP by fitting a plane over manually marked landmark points. On the other hand, existing automatic methods identify MSP by looking for a symmetric plane that divides the skull into the left and right sides. Unfortunately, this approach is inaccurate because extensive anthropological studies show that there is significant lateral asymmetry in the skulls. This paper proposes an automatic, accurate, and robust method for identifying FP and MSP of skulls. It registers a template skull model with known landmarks to a target skull to locate the landmarks, FP, and MSP on the target skull. Then, it iteratively refines the landmark locations, FP and MSP according to their medical definitions. Test results show that the proposed algorithm is more robust and accurate than symmetry-based methods. Moreover, it can also be applied to partial skull models of real patients.