BACKGROUND: Patients with rare diseases have limited access to useful information to guide treatment decisions. Engagement of patients and other stakeholders in clinical research may help to ensure that research efforts in rare diseases address relevant clinical questions and patient-centered health outcomes. Rare disease organizations may provide an effective means to facilitate patient engagement in research. However, the effectiveness of patient-engagement approaches, particularly for the study of rare diseases, has not been well studied. OBJECTIVES: To synthesize evidence about engagement of patients and other stakeholders in research on rare diseases, including the role of rare disease organizations in facilitating patient-centered research. METHODS/RESEARCH DESIGN: A systematic review and gray literature search were guided by a technical expert panel composed of patient representatives, clinicians, and researchers. English-language studies that engaged patients or other stakeholders in research on rare diseases or evaluated engagement were included. Studies were assessed on how well key research questions were answered, based on the level of detail describing engagement activities and whether outcomes from engagement were assessed. RESULTS: Thirty-five studies were included, although many reported minimal information on engagement. Patients and other stakeholders were most commonly engaged to identify patient-centered research agendas, to select which study outcomes were important to patients, to provide input on study design, and to identify strategies for increasing enrollment in trials. Rare disease organizations mainly helped provide access to patients and communicated research opportunities and findings. They also helped promote collaborative networks and provided financial support for research infrastructures. Although authors reported benefits of engagement and identified changes to their research processes, no empirical assessments of engagement practices and their effectiveness were found. CONCLUSIONS: Researchers studying rare diseases can obtain patient input regarding which research questions and health outcomes to study; however, the most effective approaches to engagement have not been well defined.