Biomedical robotic applications with accuracy requirements demand real-time position and orientation tracking, such as in the field of human motion tracking, rehabilitation, surgical instrument tracking, among many others. Among the state-of-the-art tracking technology, magnetic sensing method is an effective technology to provide fast and accurate tracking result without suffering from occlusion drawbacks. Magnetic sensing techniques are used to sense the distribution of a magnetic source field. With the sensing signals, the pose (position and orientation) between the sensor(s) and the source(s) can be estimated according to the magnetic field distribution model. In contrast to other optical tracking technologies in the clinical setup, magnetic sensing has no line-of-sight problem and is easy to be embedded with many instruments. Therefore, it is useful in intracorporeal applications to provide the location information of the tracked targets inside the human body. For this reason, magnetic sensing techniques have potential to further improve the applications of computer assisted surgeries. For example, flexible curvilinear manipulators or endoscopic devices nowadays need to be tracked in real time for better and safer operations. This chapter gives an overview of how the magnetic sensing technology works in the field of medical instrument tracking. After that, the sensing applications will be given in detail. Three typical medical applications will be discussed: (1) magnetic sensing for wireless capsule robots; (2) Current magnetic sensing devices in clinic setups; and (3) magnetic sensing for flexible surgical robots.