An automated system for navigating a medical device through the lumens and cavities in an operating region in a patient. The system includes an elongate medical device, having a proximal end and a distal end adapted to be introduced into the operating region. The system also includes an imaging system for displaying an image of the operating region, including a representation of the distal end of the medical device in the operating region. The system also includes a localization system for determining the position of the medical device in a frame of reference translatable to the displayed image of the imaging system. Finally, the system includes a system for orienting the medical device in a selected direction in the operating region, this system may be, for example, a magnetic navigation system which acts through the interaction of magnetic fields associated with the medical device inside the operating region and at least one external source magnet outside the patient's body.