Systems and methods for registration and navigation using a 3D tracking sensor are shown and described. The systems and methods utilize a 3D tracking sensor coupled to a portable surgical element to track a trackable element fixed to an object. The pose of the trackable element is determined based at least in part on information provided by the 3D tracking sensor, and the object is registered to a three-dimensional representation of the object. The 3D tracking sensor can also be used to track various objects during a surgical procedure.