Purpose: To describe a transperineal ultrasound-guided technique for implantation of electromagnetic transponders into the prostatic fossa. Methods and Materials: Patients were placed in the dorsal lithotomy position, and local anesthetic was administered. On ultrasound, the bladder, urethra, vesicourethral anastomosis, rectum, and the prostatic fossa were carefully identified. Three transponders were implanted into the prostatic fossa under ultrasound guidance in a triangular configuration and implantation was verified by fluoroscopy. Patients underwent computed tomography (CT) simulation approximately 1 week later. All patients in this study were subsequently treated with intensity modulated radiation therapy (IMRT) to the prostatic fossa. Results: From 2008 to 2012, 180 patients received transperineal implantation of electromagnetic transponders into the prostatic fossa and subsequently received IMRT. There were no cases of severe hematuria or rectal bleeding requiring intervention. There were no grade 3 or 4 toxicities. Three patients (1.7%) had a transponder missing on the subsequent CT simulation. Thirteen patients (7.3%) had transponder migration with a geometric residual that exceeded 2 mm for 3 consecutive days (5.6%) or rotation that exceeded 10 degrees for 5 consecutive days (1.7%). These patients underwent a resimulation CT scan to identify the new transponder coordinates. Conclusions: A transperineal technique for implantation of electromagnetic transponders into the prostatic fossa is safe and well tolerated, with no severe toxicity after implantation. There is a low rate of transponder loss or migration.