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Abstract Prolonged civil war and unrest has dominated the short history of South Sudan resulting in the long-term displacement of millions of people since the 1990s. Since December 2013, over one million South Sudanese refugees have fled into Uganda. International and national responses to the refugee influx in the country has been managed through parallel and integrated care and assistance mechanisms. In order to enhance effectiveness and responsiveness of assistance programmes to refugees and host communities in the country, governments and aid agencies should promote the integration of services.