Objective: To develop a method to measure intraoperative surgical instrument motion. This model will be applicable to the study of surgical instrument kinematics including surgical training, skill verification, and the development of surgical warning systems that detect aberrant instrument motion that may result in patient injury. Design: We developed an algorithm to automate derivation of surgical instrument kinematics in an endoscopic endonasal skull base surgery model. Surgical instrument motion was recorded during a cadaveric endoscopic transnasal approach to the pituitary using a navigation system modified to record intraoperative time-stamped Euclidian coordinates and Euler angles. Microdebrider tip coordinates and angles were referenced to the cadaver’s preoperative computed tomography scan allowing us to assess surgical instrument kinematics over time. A representative cadaveric endoscopic endonasal approach to the pituitary was performed to demonstrate feasibility of our algorithm for deriving surgical instrument kinematics. Conclusions: Technical feasibility of automatically measuring intraoperative surgical instrument motion and deriving kinematics measurements was demonstrated using standard navigation equipment.