Electromagnetic transponders as markers are used to localize and guide orthopedic procedures including: knee replacement, hip replacement, shoulder replacement, damaged bone reconstruction, and spine surgery, and more particularly, to guide orthopedic surgical navigation and alignment techniques and instruments. For example, the marker could further be used in any number of guides or templates that attach to the bony anatomy; such as a surgical guide, cutting guide, cutting jig, resection block and / or resurfacing guide. Further, the marker could be incorporated into an existing intramedullary guide rod for a femur and an extramedullary guide rod for a tibia in a knee replacement surgery; or into an external surgical guide system, or the marker could eliminate the need for an external template altogether. According to yet another anticipated use of the tracking system, the marker could be used in conjunction with or replace an optical alignment system.