BackgroundHumanitarian health assistance programmes have expanded from temporary approaches addressing short-term needs to providing long-term interventions in emergency settings. Measuring sustainability of humanitarian health services is important towards improving the quality of health services in refugee settings.ObjectiveTo explore the sustainability of health services following the repatriation of refugees from the west Nile districts of Arua, Adjumani and Moyo.MethodsThis was a qualitative comparative case study conducted in three west Nile refugee-hosting districts of Arua, Adjumani, and Moyo. In-depth interviews were conducted with 28 purposefully selected respondents in each of the three districts. Respondents included health workers and managers, district civic leaders, planners, chief administrative officers, district health officers, project staff of aid agencies, refugee health focal persons and community development officers.ResultsThe study shows that in terms of organization capacity, the District Health Teams provided health services to both refugee and host communities with minimal support from aid agencies. Health services were available in most former refugee hosting areas in Adjumani, Arua and Moyo districts. However, there were several disruptions notably reduction and inadequate services due to shortage of drugs and essential supplies, lack of health workers, and closure or relocation of health facilities in around former settlements. To minimize disruptions the district health office reorganized health services. In restructuring health services, the district local governments closed or upgraded health facilities to address reduced capacity and catchment population. Health workers employed by aid agencies were recruited into government services while others who were deemed excess or unqualified were laid off. Equipment and machinery including machines and vehicles were transferred to the district health office in specific health facilities. Funding for health services was mainly provided by the Government of Uganda through the Primary Health Care Grant. Aid agencies, however, continued to provide minimal support health services for refugees who remained in Adjumani district.ConclusionOur study showed that while humanitarian health services are not designed for sustainability, several interventions continued at the end of the refugee emergency in the three districts. The embeddedness of the refugee health services in the district health systems ensured health services continued through public service delivery structures. It is important to strengthen the capacity of the local service delivery structures and ensure health assistance programmes are integrated into local health systems to promote sustainability.