Background <p>The bioethical principle of respect for patients' autonomy should be implemented in every area of health care. The German rehabilitation system has some characteristics (e.g. the prevalence of inpatient rehabilitation) that make the topic particularly relevant. The aim of the study is to determine the current state of respecting patient autonomy in inpatient medical rehabilitation in Germany and to identify barriers and promoting factors from the perspective of relevant groups.</p> Methods <p>A multi-center, prospective, cross-sectional study is being conducted, including interviews with patients (<i>n</i> = 24), interviews with professionals (<i>n</i> = 21) and a survey of medical directors (<i>n</i> = 900). The empirical findings are then reviewed in three validation workshops. In addition, consensus recommendations for practice are derived by means of a Delphi process with experts (<i>n</i> = 30).</p> Discussion <p>This study will address an important gap in the empirical literature by identifying the current state and needs of patients, professionals and medical directors of rehabilitation clinics regarding the practice of respecting patient autonomy in inpatient medical rehabilitation in Germany. It is expected that the results can contribute to coming closer to the ideal of respect for patient autonomy in rehabilitation practice.</p> Trial registration <p>The study was registered with the German Clinical Trials Registry (ID: DRKS00035893).</p>