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Abstract: Background: Transcranial Magnetic Stimulation (TMS) is based on a changing magnetic field inducing an electric field in the brain. Conventionally, the TMS coil is mounted to a static holder and the subject is asked to avoid head motion. Additionally, head resting frames have been used. In contrast, our robotized TMS system employs active motion compensation (MC) to maintain the correct coil position. Objective/hypothesis: We study the effect of patient motion on TMS. In particular, we compare different coil positioning techniques with respect to the induced electric field. Methods: We recorded head motion for six subjects in three scenarios: (a) avoiding head motion, (b) using a head rest, and (c) moving the head freely. Subsequently, the motion traces were replayed using a second robot to move a sensor to measure the electric field in the target region. These head movements were combined with 2 types of coil positioning: (1) using a coil holder and (2) using robotized TMS with MC. Results: After 30 min the induced electric field was reduced by 32.0% and 19.7% for scenarios (1a) and (1b), respectively. For scenarios (2a)\–(2c) it was reduced by only 4.9%, 1.4% and 2.0%, respectively, which is a significant improvement (P < 0.05). Furthermore, the orientation of the induced field changed by 5.5°, 7.6°, 0.4°, 0.2°, 0.2° for scenarios (1a)\–(2c).