There are increasing imperatives for patients and members of the public to engage as partners in identifying health research priorities. The use of participatory methods to engage stakeholders in health care in research prioritization is not commonly reported. This article analyses the use of World Cafés as a participatory method for research prioritization with marginalized communities in Ireland and the USA. The principles of purposeful and snowball sampling were followed in both settings and a diverse range of community and health care stakeholders participated (n = 63 Ireland and n = 55 USA). The principles for a classic World Café were employed but there were novel features in each setting as well. Stewart et al.'s (Patients' and clinicians' research priorities. Health Expect 2011; 14: 439-48, conceptual framework for patient engagement was adapted and used to comparatively analyse the strengths and weaknesses of the World Cafés, focusing on agenda setting, engagement with research processes, interactional features and outputs. Design principles for World Cafés were found to align with high-quality patient engagement for research prioritization in both settings. They served to facilitate meaningful collaboration among stakeholder groups in research prioritization (research agenda setting) and explored research priorities (engagement with research). The café ambience, emphasis on hospitality and self-facilitation created an environment for dialogues within and across participating groups (interactional features). There was a commitment to follow-up actions with reference to possible subsequent research (outputs). The World Café is a valuable, participatory, flexible method that can be used with community and health care stakeholders for research prioritization with marginalized communities.