BACKGROUND. To describe 3D shoulder joint movements, the International Society of Biomechanics (ISB) recommends using segment coordinate systems (SCSs) on the humerus, scapula and thorax, and joint coordinate systems (JCSs) on the shoulder. However, one of the remaining problems is how to define the zero angles when the arm is in an initial reference position. The aim of this paper is to compare various methods of determining the JCSs of the shoulder that make it possible to define the zero angles of the arm in the resting position. METHODS. Able-bodied subjects performed elevation movements in the scapular plane, specifically neutral, internal and external rotations of the humerus. The initial humerus position (at the beginning of the arm movement) and range of motion were analysed for the purpose of clinical interpretation of arm attitude and movement. The following four different JCSs were explored: (1) the standard JCS, defined as recommended by the ISB, (2) a first aligned JCS, where the humerus SCS is initially aligned with the scapula SCS, (3) a second aligned JCS, where the opposite operation is performed and 4) a third aligned JCS, where both the humerus and the scapular SCS are initially aligned with the thorax SCS. FINDINGS. The second aligned JCS was the only method that did not produce any exaggerated range of movement in either anatomical plane. INTERPRETATION. Mathematical JCS alignment allows clearer clinical interpretation of arm attitude and movement.