This chapter describes issues related to the fundamental problem of tracking calibrated surgical instruments in MR and AR surgical applications. Many tracking and calibration problems can be solved via rigid registration or rigid registration with scaling. Framing tracking and calibration problems as registration problems admits the use of the wide range of techniques described in the registration literature. Registration error estimation techniques can be used to understand tracking and calibration errors, optimize tracking pose, and optimize the collection of calibration measurements. Registration algorithms can be used to solve pose estimation problems that occur in optical tracking and many calibration problems. This chapter provides a brief overview of tracking technologies, error estimation, and numerical solutions of registration problems that occur in calibration and tracking. Four calibration problems and their relationship to tracking and registration are described.