The invention relates to a method for designing a patient-specific registration instrument (10) for use in osteotomies, comprising the steps of- Acquiring a three-dimensional model of a fractured bone (24), wherein the fractured bone (24) is broken in a plurality of fragments (20, 20', 20") that are at least partially disjoint;- Determining a first surface portion (21) of one fragment (20), wherein the first surface portion (21) comprises a pathological surface of the fragment (20), and determining a second surface portion (22) of the fragment (20), wherein the second surface portion (22) comprises a non-pathological bone surface;- Designing a registration instrument (10) comprising a first and a second contact surface (11, 12), wherein the first contact surface (11) is an inverse surface of the first surface portion (21) of the fragment (20) and wherein the second contact surface (12) is an inverse surface of the second surface portion (22) of the fragment (20), wherein the first and second contact surface (11, 12) are configured such that the registration instrument (10) fits to the fragment only if the first and second contact surface are aligned with the first and second surface portion of the fragment.The invention also relates to a surgical tool system comprising a registration instrument (10) and an osteosynthesis plate (40).