Miniaturized, five and six degrees-of-freedom magnetic sensors, responsive to pulsed DC magnetic fields waveforms generated by multiple transmitter options, provide an improved and cost-effective means of guiding medical instruments to targets inside the human body. The end result is achieved by integrating DC tracking, 3D reconstructions of pre-acquired patient scans and imaging software into a system enabling a physician to internally guide an instrument with real-time 3D vision for diagnostic and interventional purposes. The integration allows physicians to navigate within the human body by following 3D sensor tip locations superimposed on anatomical images reconstructed into 3D volumetric computer models. Sensor data can also be integrated with real-time imaging modalities, such as endoscopes, for intrabody navigation of instruments with instantaneous feedback through critical anatomy to locate and remove tissue. To meet stringent medical requirements, the system generates and senses pulsed DC magnetic fields embodied in an assemblage of miniaturized, disposable and reposable sensors functional with both dipole and co-planar transmitters.