Background The Philippines continues its efforts in addressing inequalities in healthcare access and improving health outcomes. In order to do this, the country must also improve its knowledge base through health policy and system researches. The Department of Health's initiative to systematically determine the Medium Term Research Agenda is a purposive effort in identifying research priorities that are needed to fill knowledge gaps relevant to the achievement of universal health care. For 2014–2016, the Health Policy Development and Planning Bureau (HDPBP) and its Research Reference Hub (RRH) employed a more strategic approach to its agenda determination.

Objectives The objective of employing a systematic agenda setting was to determine strategic and coherent health policy and system research priorities for the medium-term through a consultative and evidence-based process, informed by the current research situation in this field of study.

Methods There were three phases to this agenda setting approach. The desk review assembled pertinent information on the research gaps according to health systems thematic grouping following the framework of Shakarishvili et al (2011). The review provided the platform for the second phase of discussion among topic technical experts to guide the identification of research gap priorities. Finally, the shortlist of research topics were vetted in a series of prioritization exercises with members of the RRH and the Secretary of Health, to confirm the list of medium term research agenda.

Result The process yielded a total of 18 topics divided into four health system components: (1) Health Financing Systems (7 topics), (2) Health Services (3 topics) (3) Governance and Stewardship (4 topics) and, (4) Monitoring and Evaluation (ME)/Health Information Systems (HIS) (4 topics). The exercise was able to draw in key experts from these fields and they were able to provide input on which topics should be prioritized. The succeeding vetting exercise that happened at two levels, the RRH and the Secretary of Health, confirmed the importance of the topics, which were further merged into 11 strategic ones in the context of Universal Health Care.

Conclusion A health systems research prioritization process that is guided by the use of evidence is important in order to generate information that address issues in health care access and outcomes. Some important recommendations from this exercise include the: (1) Strengthening the rigor of agenda-setting exercise in the use of current and relevant data (2) Identifying and involving a wider range of stakeholders who can be technical resource in this process and (3) Institutionalizing the process such that the quality of research agenda improves in each iteration.