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Scapulothoracic movements are altered after stroke, with resulting shoulder dysfunction. The scapulohumeral rhythm (SHR) is complex and poorly studied. Magnetic inertial measurement units (MIMUs) allow a rapid and accurate analysis of shoulder kinematics. MIMUs were used to assess the SHR during active shoulder flexion and abduction of over 60°. SHR values obtained from the hemiplegic shoulders of stroke patients (n = 7) were compared with those from healthy controls (n = 25) and correlated with clinical–functional measurements. The impairment of paretic arms was assessed using the Fugl-Meyer Assessment (FMA). We found that in paretic shoulders, the scapular tilt was significantly lower at maximal arm flexion and at 60° and 90° of arm abduction. On the paretic side, the SHR was also consistently lower for all measured arm movements. The FMA was correlated with the scapular anterior–posterior tilt at 60° and 90° of shoulder abduction (Rho = 0.847, p = 0.016, and Rho = 0.757, p = 0.049, respectively). This pilot study demonstrates the feasibility of MIMUs in assessing SHR in stroke patients and confirms previous findings on scapular dysfunction in stroke patients.