BACKGROUND: Access to HIV and malaria control programmes for refugees and internally displaced persons (IDPs) is not only a human rights issue but a public health priority for affected populations and host populations. The primary source of funding for malaria and HIV programmes for many countries is the Global Fund to Fight AIDS, Tuberculosis and Malaria (Global Fund). This article analyses the current HIV and malaria National Strategic Plans (NSPs) and Global Fund approved proposals from rounds 1-8 for countries in Africa hosting populations with refugees and/or IDPs to document their inclusion. METHODS: The review was limited to countries in Africa as they constitute the highest caseload of refugees and IDPs affected by HIV and malaria. Only countries with a refugee and/or IDP population of > or = 10,000 persons were included. NSPs were retrieved from primary and secondary sources while approved Global Fund proposals were obtained from the organisation's website. Refugee figures were obtained from the United Nations High Commissioner for Refugees' database and IDP figures from the Internal Displacement Monitoring Centre. The inclusion of refugees and IDPs was classified into three categories: 1) no reference; 2) referenced; and 3) referenced with specific activities. FINDINGS: A majority of countries did not mention IDPs (57%) compared with 48% for refugees in their HIV NSPs. For malaria, refugees were not included in 47% of NSPs compared with 44% for IDPs. A minority (21-29%) of HIV and malaria NSPs referenced and included activities for refugees and IDPs. There were more approved Global Fund proposals for HIV than malaria for countries with both refugees and IDPs, respectively. The majority of countries with > or =10,000 refugees and IDPs did not include these groups in their approved proposals (61%-83%) with malaria having a higher rate of exclusion than HIV. INTERPRETATION: Countries that have signed the 1951 refugee convention have an obligation to care for refugees and this includes provision of health care. IDPs are citizens of their own country but like refugees may also not be a priority for Governments' NSPs and funding proposals. Besides legal obligations, Governments have a public health imperative to include these groups in NSPs and funding proposals. Governments may wish to add a component for refugees that is additional to the needs for their own citizens. The inclusion of forcibly displaced persons in funding proposals may have positive direct effects for host populations as international and United Nations agencies often have strong logistical capabilities that could benefit both populations. For NSPs, strong and concerted advocacy at global, regional and country levels needs to occur to successfully ensure that affected populations are included in their plans. It is essential for their inclusion to occur if we are to reach the stated goal of universal access and the Millennium Development Goals.