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Somalia, Kenya and Ethiopia, situated in the Horn of Africa, are highly vulnerable to climate change, which manifests itself through increasing temperatures, erratic rains and prolonged droughts. Millions of people have to flee from droughts or floods either as cross-border refugees or as internally displaced persons (IDPs). The aim of this study was to identify knowledge status and gaps regarding public health consequences of large-scale displacement in these countries. After a scoping review, we conducted qualitative in-depth interviews during 2018 with 39 stakeholders from different disciplines and agencies in these three countries. A validation workshop was held with a selection of 13 interviewees and four project partners. Malnutrition and a lack of vaccination of displaced people are well-known challenges, while mental health problems and gender-based violence (GBV) are less visible to stakeholders. In particular, the needs of IDPs are not well understood. The treatment of mental health and GBV is insufficient, and IDPs have inadequate access to essential health services in refugee camps. Needs assessment and program evaluations with a patients' perspective are either lacking or inadequate in most situations. The Horn of Africa is facing chronic food insecurity, poor population health and mass displacement. IDPs are an underserved group, and mental health services are lacking. A development approach is necessary that moves beyond emergency responses to the building of long-term resilience, the provision of livelihood support and protection to reduce displacement by droughts.