A system for navigating a medical device is provided. In one embodiment, a magnetic field generator assembly generates a magnetic field. Position sensors on the medical device, on an imaging system and on the body generate signals indicative of the positions within the magnetic field. The generator assembly and reference sensors are arranged such that a correlation exists between them and the positions of the body and of a radiation emitter and a radiation detector of the imaging system. An electronic control unit (ECU) determines, responsive to signals generated by the sensors, a position of the medical device, a position of one of the radiation emitter and detector and a distance between the emitter and detector. Using this information, the ECU can, for example, register images from the imaging system in a coordinate system and superimpose an image of the device on the image from the imaging system.