Surgical navigation systems are currently used to guide the surgeon in the correct alignment of the implant. The aim of this study was to expand the use of navigation systems by proposing a surgical protocol for intraoperative kinematics evaluations during knee arthroplasty. The protocol was evaluated on 20 patients, half undergoing unicondylar knee arthroplasty (UKA) and half undergoing posterior-substituting, rotating-platform total knee arthroplasty (TKA). The protocol includes a simple acquisition procedure and an original elaboration methodology. Kinematic tests were performed before and after surgery and included varus/valgus stress at 0 and 30 degrees and passive range of motion. Both UKA and TKA improved varus/valgus stability in extension and preserved the total magnitude of screw-home motion during flexion. Moreover, compared to preoperative conditions, values assumed by tibial axial rotation during flexion in TKA knees were more similar to the rotating patterns of UKA knees. The analysis of the anteroposterior displacement of the knee compartments confirmed that the two prostheses did not produce medial pivoting, but achieved a postoperative normal behavior. These results demonstrated that proposed intraoperative kinematics evaluations by a navigation system provided new information on the functional outcome of the reconstruction useful to restore knee kinematics during surgery.