Patients are increasingly involved in agenda setting in health research policy, but little is known about whether or not patients' topics are translated into a funding programme and taken up by researchers. A qualitative evaluation of nine multi-stakeholder agenda-setting projects in the Netherlands was conducted. Document study and 54 semi-structured interviews with stakeholders were undertaken. Three strategies for the translation of research agendas into research programmes were identified: first, one-on-one translation; second, agendas were used to adapt general policies; and third, no translation. A number of factors, facilitating or impeding this translation, were identified, relating to the context or the process of programming and implementation. Context appeared to be crucial: positive attitudes towards patient involvement, good relations between stakeholders and supportive characteristics of organizations. Patient involvement was rarely sustained during programming and implementation. These insights contribute to more effective procedures for programming and implementing research agendas.