WHO GeoNetwork provides the geo-referenced data of health facilities in various countries. For example, if you enter "Madagascar" in the search field on the top left part of the web page, you can obtain the location of various health facilities in Madagascar in 2002.
As of November 2009, the following countries in Africa have this data: Benin, Botswana, Burkina Faso, Burundi, Cameroon, Comoros, Congo-Kinshasa, Cote d'Ivoire, Djibouti, Eritrea, Ethiopia, Ghana, Guinea, Kenya, Madagascar, Malawi, Mali, Mauritania, Morocco, Mozambique, Namibia, Niger, Sao Tome and Principe, Senegal, Seychelles, Somalia, South Africa, Sudan, Togo, Tunisia, Uganda, Zimbabwe.
Of course, there are caveats. There may be new health facilities created after the year these data refer to. Some facilities in the data may not be functioning due to the absenteeism of doctors and nurses.