The system and method for tracking the position of handheld medical instruments provides for instantaneous feedback and instruction to a medical practitioner during performance of a medical procedure. The system and method utilize a graphical user interface, which displays data related to at least a portion of a patients body. The user then selects a body part of the patient for performing a selected medical procedure. A plurality of pulse receivers are provided for detecting and receiving very narrow pulse electromagnetic pulses. A plurality of instrument pulse emitters are mounted on a handheld medical instrument for selectively transmitting first very narrow pulse electromagnetic pulses, and a to plurality of patient pulse emitters are positioned on the selected body part of the patient for selectively transmitting second very narrow pulse electromagnetic pulses. The position and orientation of the handheld medical instrument with respect to the selected body part is then determined.
