CIA activities in Africa
This article deals with activities of the U.S. Central Intelligence Agency (CIA) in Africa. Be advised this list may be incomplete due to the clandestine nature of the activities described.
This NIE projects Western security interests for 3-5 years from 1965. "Political and social turmoil is virtually certain during the period of this estimate in most of the states of Sub-Saharan Africa. The general trend in the area--to which there are some exceptions--is probably toward more radical policies, and certainly toward more vigorous manifestations of African nationalism, in a variety of forms.
"The various "liberation" movements in white-dominated southern Africa have made little headway despite considerable emotional support elsewhere in Africa. Meanwhile, white resistance has stiffened. Although most independent African states, as well as the USSR and China, probably will step up assistance to the nationalists, it is almost certain that white governments will command sufficient power and determination to contain "liberation" movements at least for the period of this estimate.
"Economic growth in most areas will be very slow, with setbacks are probable ...There is a desperate shortage of virtually all kinds of technical and managerial skills; indeed, the basic institutions and staff for economic development are often inadequate or absent. ..ot is highly unlikely that most African countries will obtain external assistance or investment on anything approaching the scale required for sustained economic development.
"Communists have made substantial progress in expanding their presence in Africa, and the situation will provide them with new opportunities. Western influence in Africa will remain important during the period of this estimate, but it will decline, in part because both the UK and France will gradually shed presently expensive commitments. There is a good chance that a few African states will collaborate closely with either Moscow or Peiping, and become, at least temporarily, highly unfriendly to the West... However, even the militant radicals prize their freedom of movement, and we consider it unlikely that any African country will become a full-fledged Communist state, or will reject all ties with the West.
"African relations with the US will remain ambivalent and difficult. Nevertheless, we do not believe that in most instances difficulties will decisively affect such material interests as the US has in Africa. No African raw materials or other resources are essential to US security. The US is likely to be able to retain the Kagnew facility (A NSA intercept station) at least during Haile Selassie's lifetime. Other less important installations and privileges seem safe during the period of this estimate. 
The Democratic Republic of the Congo and Tanzania, though more commonly reckoned in Central and Eastern Africa respectively, are occasionally included in Southern Africa. The Southern African Development Community (SADC) was established in 1980 to facilitate co-operation in the region. The Southern African Customs Union (SACU), created in 1969, comprises the five countries in the UN subregion of Southern Africa.
There are a number of situations in East Africa where there are no simple rules about balancing internal, regional, and worldwide interests. At various times, Sudan has been involved in the north-south Second Sudanese Civil War, the humanitarian crisis in Darfur, and alternately hosting and ousting transnational Islamic extremists.
Another multipolar conflict involves Ethiopia, the breakaway country of Eritrea, and Somalia, the latter generally considered a failed state but beginning to establish structure. Ethiopia has been considered the US proxy.
There may have been CIA involvement with these various countries and regions, less from their internal and neighbor disputes, and more in dealing with transnational terrorism. It is not a simple situation, whether considered morally, geopolitically, or with respect to alliances.
East Africa 1971
An 1971 NIE discussed a number of regional issues:  This document defined East Africa to as including Kenya, Uganda, Tanzania, and Zambia. Zambia is present due to its links to Tanzania.
In the 1960s, the newly independent states of East Africa seemed to be off to a promising start. Under national rulers of considerable stature, the countries set about devising means of developing their societies and economies in an atmosphere of relative political stability. The brief army mutinies of 1964, which simultaneously afflicted Uganda, Kenya, and Tanzania,) were quickly sup-pressed with assistance from the UK and appeared to have a salutary effect on government relations with the military. In colonial times, the UK had established common transportation, communications, and monetary services for Kenya, Tanganyika, and Uganda. In 1967, these services were consolidated in an East African Community (EAC). Each of the national rulers confronted and over-came internal political challenges. President Kenneth Kaunda's leadership qualities were tested by adversities, and his friendship with President Julius Nyerere of Tanzania helped bring Zambia much closer to the EAC.The euphoria of this immediate, post-independence period has since given way to frustration and disappointment. The rulers of East Africa, like their counterparts else-where on the continent, have gradually found themselves confronted with a host of worsening problems... Domestic pressures, mutual suspicions of the national leaders, and the uneven patterns of development of the various economies have led to more nationalistic postures in foreign relations. Though spared the civil strife which afflicted Nigeria and the "revolving door" presidential changes of small West African states, East Africa is clearly passing through a period of change and challenge in which former arrangements and agreements are under increasing pressure.
Much of the region's politics is related to the overthrow of Uganda's President Milton Obote by General Idi Amin in January 1971, followed by a personal and ideological conflict between Amin and Nyerere of Tanzania. It has contributed to an atmosphere of distrust among other African leaders in the area who also lean towards simplistic views of foreign relations (i.e., seeing neighbors as pro-Arab or anti-Arab, pro-Communist or anti-Communist). President Mobutu of Congo (Kinshasa) has talked with Amin about creating a belt of anti-Arab, anti-Communist nations (Ethiopia, Kenya, Uganda, and the Congo) to stem the southward flow of radicalism, which they fear, and to isolate Nyerere and Kaunda. Though no formal arrangements are in the cards, a variety of bilateral ties tend to bring the conservative states together. Kenya is providing assistance to the Ugandan security services. Kenya and Ethiopia have defense agreements against Somali irrendentist efforts. Uganda, Congo (Kinshasa), and Ethiopia are supporting the southern Sudanese in their struggle against Khartoum and are cooperating in various ways, but for different reasons, with the Israelis.
East Africa 2006
Another regional problem  involves effects on Kenya, Tanzania, and Uganda as "blowback" from the United States War on Terrorism in the Horn of Africa and the US proxy, Ethiopia. The Somalia conflict has increased the flow of weapons into Kenya and Uganda, spawned a regional polio epidemic, destabilized the relationship between Kenya and Somalia, increased tension within Kenya’s Muslim community, and created the possibility of an expanded regional conflict.
"Ethiopia, in an effort to support Somalia’s Transitional Federal Government (TFG) against the Islamic Courts Union (ICU), pushed into Somalia to retake the town of Bur Haquba near Baidoa. This sparked calls by the ICU for a Jihad against Ethiopia. To support Ethiopia, US Assistant Secretary of State for African Affairs Jendayi Frazer at week’s end then accused Eritrea of supporting the ICU.
- "National Intelligence Estimate 60/70-65: Problems and Prospects in Sub-Saharan Africa". Foreign Relations of the United States, 1964-1968, Volume XXIV,Africa. April 22, 1965. FRUS-XXIV-195, NIE 60/70-65. all the countries of Africa except the following: UAR, Sudan, Libya, Algeria, Morocco, Tunisia, and Spanish Sahara
- Central Intelligence Agency (7 October 1971). NIE 70-71: Troubles in East Africa. Foreign Relations of the United States, 1969-1976, Volume E-5, Documents on Africa, 1969-1972. United States Department of State. FRUS E-5 No. 288.
- Church, William (2006-10-23). "Somalia: CIA Blowback Weakens East Africa".