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Brain-Computer Interfaces (BCIs) process brain activity in real time, and mediate non-muscular interaction between and individual and the environment. The subserving algorithms can be used to provide a quantitative measurement of physiological or pathological cognitive processes - such as Motor Imagery (MI) - and feed it back the user. In this paper we propose the clinical application of a BCI-based rehabilitation device, to promote motor recovery after stroke. The BCI-based device and the therapy exploiting its use follow the same principles that drive classical neuromotor rehabilitation, and (i) provides the physical therapist with a monitoring instrument, to assess the patient's participation in the rehabilitative cognitive exercise; (ii) assists the patient in the practice of MI. The device was installed in the ward of a rehabilitation hospital and a group of 29 patients were involved in its testing. Among them, eight have already undergone a one month training with the device, as an add-on to the regular therapy. An improved system, which includes analysis of Electromyographic (EMG) patterns and Functional Electrical Stimulation (FES) of the arm muscles, is also under clinical evaluation. We found that the rehabilitation exercise based on BCI mediated neurofeedback mechanisms enables a better engagement of motor areas with respect to motor imagery alone and thus it can promote neuroplasticity in brain regions affected by a cerebrovascular accident. Preliminary results also suggest that the functional outcome of motor rehabilitation may be improved by the use of the proposed device.