A method for selecting electroencephalographic (EEG) signals in motor imagery-based brain-computer interfaces (MI-BCI) is proposed for enhancing the online interoperability and portability of BCI systems, as well as user comfort. The attempt is also to reduce variability and noise of MI-BCI, which could be affected by a large number of EEG channels. The relation between selected channels and MI-BCI performance is therefore analyzed. The proposed method is able to select acquisition channels common to all subjects, while achieving a performance compatible with the use of all the channels. Results are reported with reference to a standard benchmark dataset, the BCI competition IV dataset 2a. They prove that a performance compatible with the best state-of-the-art approaches can be achieved, while adopting a significantly smaller number of channels, both in two and in four tasks classification. In particular, classification accuracy is about 77–83% in binary classification with down to 6 EEG channels, and above 60% for the four-classes case when 10 channels are employed. This gives a contribution in optimizing the EEG measurement while developing non-invasive and wearable MI-based brain-computer interfaces.