Motion capture (Mocap) systems are considered more and more interesting for the assessment of rehabilitation processes. In fact, medical personnel are increasingly demanding for technologies (possibly low-cost) to quantitatively measure and assess patients’ improvements during rehabilitation exercises. In this paper, we focus the attention on the assessment of rehabilitation process for injured shoulders. This is particularly challenging because the recognition and the measurement of compensatory movements are very difficult during visual assessment and the movements of a shoulder are complex and arduous to be captured. The proposed solution integrates a low-cost Mocap system with video processing techniques to allow a quantitative evaluation of abduction, which is one of the first post-surgery exercises required for shoulder rehabilitation. The procedure is based on a set of open-source software tools to measure abduction and evaluate the correctness of the movement by detecting and measuring compensatory movements according to the parameters commonly considered by the physicians. Finally, a preliminary results and future works are presented and discussed.