An endoscope tracking system includes an endoscope, at least one endoscope tracking transmitter carried by the endoscope, a plurality of anatomy mapping transmitters, a receiver communicating with the at least one endoscope tracking transmitter and the anatomy mapping transmitters and a processor communicating with the receiver. The processor is adapted to generate an anatomical map based on input from the anatomy mapping transmitters and an endoscope tracking image based on input from the at least one endoscope tracking transmitter and superimpose the endoscope tracking image on the anatomical map.