Abstract This paper describes a new methodology that enables mapping of the ligament insertion sites onto bone surfaces in the knee joint by co-registration of the data acquired using digitization and computed tomography (CT). Local coordinate systems on the distal femur and proximal tibia were established by three spherical fiducial markers rigidly affixed to each bone. The fiducial marker centroid locations were identified by a least-squares sphere-fitting algorithm. An optimization correction procedure was proposed to mitigate the effect of the target registration error (TRE) on the alignment of coordinate systems for co-registration. A test with four cadaveric specimens demonstrated successful mapping of insertion sites for five ligaments. Fiducial registration error (FRE) as measured by the differences in inter-marker distances between the two modalities was smaller than 2%. The optimization procedure corrected the insertion site invisibility or partial visibility problem and improved the overall mapping quality, as indicated by substantial reduction of the mean and dispersion of distances from digitized insertion site points to the bone surfaces.