Purpose: To validate and apply a method for the quantification of breathing-induced prostate motion (BIPM) for patients treated with radiotherapy and implanted with electromagnetic transponders for prostate localization and tracking. Methods: For the analysis of electromagnetic transponder signal, dedicated software was developed and validated with a programmable breathing simulator phantom. The software was then applied to 1,132 radiotherapy fractions of 30 patients treated in supine position, and to a further 61 fractions of 2 patients treated in prone position. Results: Application of the software in phantom demonstrated reliability of the developed method in determining simulated breathing frequencies and amplitudes. For supine patients, the in vivo analysis of BIPM resulted in median (maximum) amplitudes of 0.10 mm (0.35 mm), 0.24 mm (0.66 mm), and 0.17 mm (0.61 mm) in the left-right (LR), cranio-caudal (CC), and anterior-posterior (AP) directions, respectively. Breathing frequency ranged between 7.73 and 29.43 breaths per minute. For prone patients, the ranges of the BIPM amplitudes were 0.1-0.5 mm, 0.5-1.3 mm, and 0.7-1.7 mm in the LR, CC, and AP directions, respectively. Conclusions: The developed method was able to detect the BIPM with sub-millimeter accuracy. While for patients treated in supine position the BIPM represents a reduced source of treatment uncertainty, for patients treated in prone position, it can be higher than 3 mm.