The biomechanical complexity of the human shoulder, while critical for functionality, poses a challenge for objective assessment during sensorimotor rehabilitation. With built-in sensing capabilities, robotic exoskeletons have the potential to serve as tools for both intervention and assessment. The bilateral upper-extremity Harmony exoskeleton is capable of full shoulder articulation, forearm flexion-extension, and wrist pronation-supination motions. The goal of this paper is to characterize Harmony's anatomical joint angle tracking accuracy towards its use as an assessment tool. We evaluated the agreement between anatomical joint angles estimated from the robot's sensor data and optical motion capture markers attached to the human user. In 9 healthy participants we examined 6 upper-extremity joint angles, including shoulder girdle angles, across 4 different motions, varying active/passive motion of the user and physical constraint of the trunk. We observed mostly good to excellent levels of agreement between measurement systems with for shoulder and distal joints, magnitudes of average discrepancies varying from 0.43° to 16.03° and width of LoAs ranging between 9.44° and 41.91°. Slopes were between 1.03 and 1.43 with r > 0.9 for shoulder and distal joints. Regression analysis suggested that discrepancies observed between measured robot and human motions were primarily due to relative motion associated with soft tissue deformation. The results suggest that the Harmony exoskeleton is capable of providing accurate measurements of arm and shoulder joint kinematics. These findings may lead to robot-assisted assessment and intervention of one of the most complex joint structures in the human body.