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Abstract Electromagnetic (EM) motion tracking systems are suitable for many research and clinical applications, including in vivo measurements of whole-arm movements. Unfortunately, the methodology for in vivo measurements of whole-arm movements using EM sensors is not well described in the literature, making it difficult to perform new measurements and all but impossible to make meaningful comparisons between studies. The recommendations of the International Society of Biomechanics (ISB) have provided a great service, but by necessity they do not provide clear guidance or standardization on all required steps. The goal of this paper was to provide a comprehensive methodology for using EM sensors to measure whole-arm movements in vivo. We selected methodological details from past studies that were compatible with the ISB recommendations and suitable for measuring whole-arm movements using EM sensors, filling in gaps with recommendations from our own past experiments. The presented methodology includes recommendations for defining coordinate systems (CSs) and joint angles, placing sensors, performing sensor-to-body calibration, calculating rotation matrices from sensor data, and extracting unique joint angles from rotation matrices. We present this process, including all equations, for both the right and left upper limbs, models with nine or seven degrees-of-freedom (DOF), and two different calibration methods. Providing a detailed methodology for the entire process in one location promotes replicability of studies by allowing researchers to clearly define their experimental methods. It is hoped that this paper will simplify new investigations of whole-arm movement using EM sensors and facilitate comparison between studies.