STUDY DESIGN: Cross-sectional. OBJECTIVES: To compare sternoclavicular, acromioclavicular, and scapulothoracic joint motion between symptomatic and asymptomatic individuals during shoulder motion performed in 3 planes of humerothoracic elevation. BACKGROUND: Differences in scapulothoracic kinematics are associated with shoulder pain. Several studies have measured these differences using surface sensors, but the results of this technique may be affected by skin-motion artifact. Furthermore, previous studies have not included the simultaneous measurement of sternoclavicular and acromioclavicular joint motion. METHODS: Transcortical bone pins were inserted into the clavicle, scapula, and humerus of 12 asymptomatic and 10 symptomatic individuals for direct, bone-fixed tracking using electromagnetic sensors. Angular positions for the sternoclavicular, acromioclavicular, and scapulothoracic joints were measured during shoulder flexion, abduction, and scapular plane abduction. RESULTS: Differences between groups were found for sternoclavicular and scapulothoracic joint positions. Symptomatic individuals consistently demonstrated less sternoclavicular posterior rotation, regardless of angle, phase, or plane of shoulder motion. Symptomatic individuals also demonstrated less scapulothoracic upward rotation at 30° and 60° of humerothoracic elevation during shoulder abduction and scapular plane abduction. CONCLUSION: The results of this study show that differences in shoulder complex kinematics exist between symptomatic and asymptomatic individuals. However, the magnitude of these differences was small, and the resulting clinical implications are not yet fully understood. The biomechanical coupling of the sternoclavicular and acromioclavicular joints requires further research to better understand scapulothoracic movement deviations and to improve manual therapy and exercise-based physical therapy interventions.