The aim of this study is to compare three methodologies of prostate localization. Daily prostate localization using cone beam CT (CBCT) or orthogonal kV imaging has been performed at UT Southwestern Medical Center since 2006. Prostate patients are implanted with gold seeds, which are matched with the planning CT or DRR before treatment. More recently, a technology using electromagnetic transponders implanted within the prostate was introduced into our clinic (Calypso®). With each technology, patients are localized initially using skin marks and the room lasers. In this study, patients were localized with Calypso and either CBCT or kV orthogonal images in the same treatment session, allowing a head-to-head comparison of the technologies. Localization difference distributions were determined from the difference in the offsets determined by CBCT/kV imaging and Calypso. CBCT-Calypso and kV imaging-Calypso localization data were summarized from over 160 and 100 fractions each, respectively. In these patients, the differences between CBCT-Calypso and kV imaging-Calypso localizations are 0.31 ± 1.82 mm, 0.00 ± 1.00 mm, -0.28 ±1.36 mm and 0.28 ± 4.12 mm, -0.28 ± 3.22 mm, 0.16 ± 1.61 mm, respectively, in the AP, SI, and RL directions. These results show excellent agreement between radiographic localization techniques and electromagnetic transponders, indicating that each of the localization techniques is accurate and suitable for prostate localization. Mean absolute localization offsets for kV imaging patients localized with Calypso are 6.98 ± 4.02 mm, 2.06 ± 3.09 mm, and 0.78 ± 3.06 mm in the AP, SI, and RL directions, indicating that the prostate is displaced approximately 7 mm posteriorly and 2 mm inferiorly when compared to localization with skin marks.