|Abstract Background Although humans spend most of their day in a standing or sitting position, it is difficult to accurately evaluate the alignment of the shoulder girdle during daily activity, and its alignment changes between positions. The purpose of this study was to evaluate the 3-dimensional alignment of the shoulder girdle in the supine and standing positions by computed tomography (CT) and to assess the alignment changes of the shoulder girdle between these two positions. Methods CT scans of both shoulders of 100 healthy volunteers were prospectively taken in both supine and standing positions on the same day. The local 3-dimensional coordinate systems of the thorax, clavicle, and scapula were defined from the specific bony landmarks, and 3-dimensional angular rotations and positions of the clavicle and scapula were calculated. Differences in rotations and positions of the clavicle and scapula were evaluated between the supine and standing positions. Results Compared with the supine position, the clavicle showed significantly less elevation and greater retraction, and the scapula showed significantly less upward rotation, anterior tilting, and internal rotation in the standing position. Compared with the supine position, the clavicle center was located more inferiorly, posteriorly, and laterally, and the scapula center was located more inferiorly, posteriorly, and medially in the standing position. Conclusions The present study showed that angular rotations and positions of the clavicle and scapula change significantly with position due to the effect of gravity.