Background: The aim of this study was to analyze differences in three-dimensional shoulder kinematics between asymptomatic subjects and patients who were diagnosed with rotator cuff tears. Methods: This cross-sectional study recruited 13 symptomatic subjects and 14 asymptomatic subjects. Data were obtained from three inertial sensors placed on the humerus, scapula and sternum. Kinematic data from the glenohumeral, scapulothoracic and thoracohumeral joints were also calculated. The participants performed shoulder abductions and flexions. The principal angles of movements and resultant vectors in each axis were studied. Results: The glenohumeral joint showed differences in abduction (p = 0.001) and flexion (p = 0.000), while differences in the scapulothoracic joint were only significant during flexion (p = 0.001). The asymptomatic group showed higher velocity values in all sensors for both movements, with the differences being significant (p < 0.007). Acceleration differences were found in the scapula during abduction (p = 0.001) and flexion (p = 0.014), as well as in the sternum only during shoulder abduction (p = 0.022). Conclusion: The results showed kinematic differences between the patients and asymptomatic subjects in terms of the mobility, velocity and acceleration variables, with lower values for the patients.