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Albeit research on brain-computer interfaces (BCI) for controlling applications has expanded tremendously, we still face a translational gap when bringing BCI to end-users. To bridge this gap, we adapted the user-centered design (UCD) to BCI research and development which implies a shift from focusing on single aspects, such as accuracy and information transfer rate (ITR), to a more holistic user experience. The UCD implements an iterative process between end-users and developers based on a valid evaluation procedure. Within the UCD framework usability of a device can be defined with regard to its effectiveness, efficiency, and satisfaction. We operationalized these aspects to evaluate BCI-controlled applications. Effectiveness was regarded equivalent to accuracy of selections and efficiency to the amount of information transferred per time unit and the effort invested (workload). Satisfaction was assessed with questionnaires and visual-analogue scales. These metrics have been successfully applied to several BCI-controlled applications for communication and entertainment, which were evaluated by end-users with severe motor impairment. Results of four studies, involving a total of N = 19 end-users revealed: effectiveness was moderate to high; efficiency in terms of ITR was low to high and workload low to medium; depending on the match between user and technology, and type of application satisfaction was moderate to high. The here suggested evaluation metrics within the framework of the UCD proved to be an applicable and informative approach to evaluate BCI controlled applications, and end-users with severe impairment and in the locked-in state were able to participate in this process.