This work improves surgical navigation by combining electromagnetic tracking and personalized guides in a novel system. Surgical navigation assists a surgeon by tracking instruments relative to the anatomy of interest, typically by optically tracking specialized markers. One recent navigation aid is a personalized guide, which is a mechanical device that is customized to a patient based on preoperative images. A small "negative surface" physically registers the guide to the patient, and typically one or more through-holes in the guide constrain a physical path during surgical drilling. A personalized guide may incorporate a surgical plan into their design but offers no means of intraoperative adjustment or correction. Electromagnetic tracking uses a small antenna that is localized within an electromagnetic field. Advantages of electromagnetic tracking include small sensor weight and not being constrained to a line of sight; drawbacks include a lower positional accuracy than optical tracking, and interference from nearby electrically conductive objects. This work is based on a paired-lines registration algorithm that was used to create tracked guides for small, delicate bony anatomy. Electromagnetically tracked guides were applied to additively manufactured bone models. The guides were compared to optical tracking in the presence of common metallic surgical instruments. In every analysis, EM-tracked guides were found to statistically significantly outperform optical tracking. A pre-clinical cadaveric case study demonstrated comparable performance to optical tracking. This work suggests that EM-tracked guides successfully combined the flexibility of tracking with the simplicity of physical registration in surgical navigation.