Background: Though alignment of the spine and lower extremities in the standing neutral position has been evaluated, a few studies evaluating the alignment of the upper extremities have also been made. This study assessed the normal alignment of the upper extremities in the standing neutral position and clarified the three-dimensional angular rotations of the upper extremity joints.Methods: Computed tomography (CT) images of 158 upper extremities from 79 healthy volunteers were prospectively acquired in the standing neutral position using an upright CT scanner. Three-dimensional coordinate systems of the thorax, scapula, humerus, and forearm were designated, and three-dimensional angular rotations of the scapulothoracic, glenohumeral, and elbow joints were calculated.Results: The mean angle of the scapulothoracic joint was 8.5° ± 5.9° of upward rotation, 28.7° ± 5.9° of internal rotation, and 7.9° ± 5.2° of anterior inclination. The mean angle of the glenohumeral joint was 4.4° ± 5.9° of abduction, 9.4° ± 12.3° of internal rotation, and 0.3° ± 4.4° of extension. The mean angle of the elbow joint was 9.6° ± 3.7° of valgus, 88.8° ± 14.3° of pronation, and 15.4° ± 4.2° of flexion. Correlations in angular rotation values were found, and interactions for keeping the upper extremities in a neutral position were observed.Conclusions: This study clarified the three-dimensional angular rotation of upper extremity joints in the standing neutral position using an upright CT scanner. Our results may provide important insights for the functional evaluation of upper extremity alignment.