Background. The purpose of this biomechanical study was to determine the effect of shortened clavicle malunion on the center of rotation of the glenohumeral (GH) joint, and the capacity of repair to restore baseline kinematics. Methods. Six shoulders underwent automated abduction (ABD) and abbreviated throwing motion (ATM) using a 7-DoF automated upper extremity testing system in combination with an infrared motion capture system to measure the center of rotation of the GH joint. ATM was defined as pure lateral abduction and late cocking phase to the end of acceleration. Torsos with intact clavicle underwent testing to establish baseline kinematics. Then, the clavicles were subjected to midshaft fracture followed by kinematics testing. The fractured clavicles underwent repairs first by clavicle length restoration with plate fixation, and then by wiring of fragments with a 2-cm overlap to simulate shortened malunion. Kinematic testing was conducted after each repair technique. Center of rotation of the GH joint was plotted across all axes to outline 3D motion trajectory and area under the curve. Results. Throughout ABD, malunion resulted in increased posterior and superior translation compared to baseline. Plate fixation restored posterior and superior translations at lower abduction angles but resulted in excess anterior and inferior translation at overhead angles. Throughout ATM, all conditions were significantly anterior and superior to baseline. Translation with malunion was situated anterior to the fractured and ORIF conditions at lower angles of external rotation. Plate fixation did not restore baseline anteroposterior or superoinferior translation at any angle measured. Conclusions. This study illustrates the complex interplay of the clavicle and the GH joint. While abnormal clavicle alignment alters shoulder motion, restoration of clavicle length does not necessarily restore GH kinematics to baseline. Rehabilitation of the injured shoulder must address the osseous injury and the dynamic forces of the shoulder girdle.