According to United Nations High Commissioner for Refugees (UNHCR), until June 2017, 65.6 million people were forcibly displaced worldwide of whom 22.5 million were refugees. Historically, health services for refugee populations have been provided primarily through dedicated health clinics located within refugee camps run by UNHCR or international non-governmental organizations. However, as patterns of mobility and emergency duration have changed, there is recognition that these parallel health services in camps are unsustainable and insufficiently benefit the surrounding host populations, many of whom are also vulnerable. Instead, UNHCR has called for the integration of refugee populations into national health systems, and the World Bank recently established a US$2 billion fund for refugee-hosting governments to support the integration of refugees and host communities, covering multiple sectors, including health. This move towards a "humanitarian-development nexus" has the potential to support refugees and nationals, while increasing the capacity of national systems. There has been limited research exploring the issue of integrating refugees into health systems and its effects on such systems. Thus, there is limited evidence available to international, regional or national actors in terms of which types of arrangements may work best in a particular context. We will conduct case studies in three different countries currently hosting large numbers of refugees: Lebanon (1.1m), Jordan (655,624), and Uganda (940,800). We plan to focus on Syrian refugees in Lebanon and Jordan, and South Sudanese refugees in Uganda. While policies in Lebanon, Jordan and Uganda have all integrated refugees into health systems to some degree, they differ widely in their approach, and in the structure of the underlying health system. We will analyse each country case separately and then seek to identify patterns across the three cases, so as to be able to draw conclusions that are relevant to other contexts. Specifically, our research will seek to understand the perceptions and experiences of stakeholders as well as host and refugee populations towards refugees' integration into national health systems including how these stakeholders understand the meaning of integration and perceive its desirability. It will identify the structural, institutional and individual/community factors that have shaped policies on integration of refugees, including refugee health workers, into national health systems. The study will also assess how the pattern and extent of refugee integration across these three contexts has affected health services received by refugee and host populations and how financial mechanisms and flows affected financial sustainability of services. We will then convene national, regional and international policy and decision-makers to reflect upon the findings from these analyses, and identify their implications for future policy and practice. Within each of the three country cases we will employ a mixed-method approach that will be tailored to match local circumstances. We plan to identify timelines for the development of refugee policies and will conduct a policy analysis to understand how policies and practices evolved and why. We will then use existing datasets and primary data collection within district level cases, to explore how different aspects of refugee integration into national health systems over time has affected availability, access to health services and quality of health care. A comparative study, across these three different contexts, will enable decision-makers within the three countries to learn from and consider alternative approaches to refugee integration, but will also provide evidence and policy recommendations that will be transferable to other existing and future refugee settings. We also seek to inform global policy and guidance on this issue, working with actors such as the UNHCR, the World Bank and WHO among others.