Closed-loop medical devices such as brain-computer interfaces are an emerging and rapidly advancing neurotechnology. The target patients for brain-computer interfaces (BCIs) are often severely paralyzed, and thus particularly vulnerable in terms of personal autonomy, decisionmaking capacity, and agency. Here we analyze the effects of closed-loop medical devices on the autonomy and accountability of both persons (as patients or research participants) and neurotechnological closed-loop medical systems. We show that although BCIs can strengthen patient autonomy by preserving or restoring communicative abilities and/or motor control, closed-loop devices may also create challenges for moral and legal accountability. We advocate the development of a comprehensive ethical and legal framework to address the challenges of emerging closed-loop neurotechnologies like BCIs and stress the centrality of informed consent and refusal as a means to foster accountability. We propose the creation of an international neuroethics task force with members from medical neuroscience, neuroengineering, computer science, medical law, and medical ethics, as well as representatives of patient advocacy groups and the public.