A method of navigating a magnet-tipped distal end of an elongate medical device through the body includes providing an image display of the part of the body through which the medical device is being navigated and using the display to input the desired path of the medical device by identifying points on the desired path on the display. The magnetic field needed to orient the end of the medical device in the direction of the desired path as indicated on the display is then determined. In one embodiment where only points on the desired path are identified, the field direction is the direction indicated by the points on the desired path.; In a second embodiment, where points on the current path and the desired path are identified, the desired angle of deflection is determined, and the direction of the magnetic field is set to lead this desired angle of deflection by 90 DEG to over torque the end of the catheter, and the intensity of the field is determined from a table of experimentally determined field intensities for given angles of deflection. The apparatus for navigating a magnet-tipped medical device through the body in accordance with the invention includes a magnet system for applying a magnetic field to the magnet-tipped distal end of the medical device to orient the distal end of the medical device; a computer for controlling the magnet system to generate a specified magnetic field in the body part; first and second imaging devices connected to the computer, for providing bi-planar images of the body part through which the medical device is being navigated; first and second displays for displaying the images from the image devices; and an input device for inputting points identifying the desired path of the medical device on each of the displays. The computer is programmed to determine the magnetic field necessary to control orient the medical device on the path input on the displays.