An assembly of a patient specific instrument and tracking system comprises a patient specific instrument having a body with a patient specific contact surface negatively shaped relative to a corresponding surface of a bone for complementary contact therewith. An inertial sensor unit with a preset orientation is connected to the body in a planned connection configuration, such that a geometrical relation between the contact surface and the inertial sensor unit is known. A tracking system has a tracking processor connected to the inertial sensor unit, a user interface, and bone orientation data related to the patient specific contact surface, the tracking processor producing orientation tracking data for the bone using the geometrical relation and the bone orientation data when the preset orientation of the inertial sensor unit is initialized, to output the orientation tracking data on the user interface.
