A new method of scoring systems for the functional assessment of the shoulder is presented. 3D accelerometers and gyroscopes attached on the humerus were used to differentiate a healthy from a painful shoulder. The method was first tested on 10 healthy volunteer subjects with no shoulder pathology. The system was then tested on 10 patients with unilateral shoulder pathology (rotator cuff disease, osteoarthritis) before and after surgery (3, 6 months). In order to evaluate the system, nine tests based on the Simple Shoulder Test (SST) were performed on each shoulder for each patient. Three scores were defined: the P score was based on the angular velocities and accelerations of the humerus; the RAV score was based only on the angular velocities of the humerus; the M score was based on the sum of all moments of the humerus. Our kinematic scores indicated significant differences between baseline and follow-up (p<0.05) and differentiated between patients with varying severity of the same condition. We demonstrated a reliable technique of evaluating shoulder pathology and the results of surgery.