Uganda's relations with its other neighbors were dominated by responses to serious domestic political conflicts within Uganda or a neighboring state that spilled over their common borders. After the NRM took power, the threat that it would support likeminded radical guerrÍÍÍÍilla movements near the border in each of Uganda's neighbors except Tanzania tinged interstate relations with deep suspicion.

Relations with Sudan had been primarily concerned with the consequences of the Sudanese civil war for the first decade after Uganda's independence. The Ugandan government regarded the war as pitting Africans against Arabs and thus tended to be sympathetic to the southern desire for secession. Thousands of southern Sudanese refugees fled to Uganda. Following the assumption of power by a left-wing Sudanese regime in 1969, Obote tilted his loyalties toward the Sudanese government in order to strengthen his own radical credentials. After this war was settled in 1972, Uganda's relations with Sudan became quieter. Many southern Sudanese took advantage of Amin's ethnic ties to southern Sudan to join the Ugandan Army and take part in its indiscriminate attacks on Ugandan civilians. When Amin was overthrown, the Sudanese soldiers, along with many Ugandan supporters of Amin, fled to southern Sudan. There they were joined by 200,000 Ugandan refugees, mostly from northwest Uganda, during Obote's second presidency, when the new Ugandan Army took revenge on them.

In 1983 a new phase began with the second Sudanese civil war, which was complicated in 1986 by an outbreak of fighting in northern Uganda between remnants of Obote's former Ugandan army and the NRA. Each government accused the other of assisting antigovernment rebels. After 1987 President Museveni became a mediator in an effort to arrange meetings in Kampala between the leaders of the warring Sudanese factions. In support of this policy, the NRM government announced that it would not export revolution and thus would not help the Sudanese rebels or give them sanctuary in Uganda. By 1990 the border had become considerably less significant in disrupting relations between the two countries because Sudanese rebels controlled most of it, because the northern Ugandan rebels who had used Sudan as a sanctuary were largely defeated, and because most of the Ugandan refugees in Sudan had returned home. In early April 1990, Sudanese ruler Lieutenant General Umar Hasan Ahmad al Bashir visited Kampala and signed a nonaggression pact with Museveni.

Rwandans had started to migrate from their overpopulated country to Uganda in search of jobs early in the colonial period. Four years before Uganda became independent, a revolution in Rwanda in which Hutu agriculturalists took power from their Tutsi (Watutsi) overlords resulted in a mass exodus of Tutsi refugees into Uganda. Many remained in camps, hoping eventually to return home, but the Rwandan government refused to accept them, claiming the country was too overcrowded. During Obote's second presidency in the 1980s, the Ugandan government regarded them as supporters of the NR d6cM. A cririsis erupted in 1982 when local officials in southwestern Uganda forced 80,000 people of Rwandan descent, including many with Ugandan citizenship, to leave their homes and possessions. Refused entry into Rwanda, they were forced to live in refugee camps on the Ugandan side of the border, where they remained through 1990. Relations with Rwanda were again strained in October 1990, when Rwandans in the NRA joined a rebel invasion of northern Rwanda. President Juvénal Habyarimana accused Museveni of supporting the Rwandan Patriotic Front, and relations worsened throughout the rest of 1990.

Uganda's involvement in rebel activity in Zaire almost brought down the Obote government in 1966, although the Ruwenzururu rebellion on the Ugandan side of the border during the 1960s attracted little support from Zaire. During the late 1980s, however, when a radical Zairian group dedicated to the overthrow of President Mobutu Sese Seko, the Congolese Liberation Party (Parti de Libération Congolaise--PLC), became active in the same mountains, Mobutu accused the NRM of supporting it. Remnants of the Ruwenzururu movement established a working relationship with the PLC in 1987, and the NRM became the enemy of both rebel movements. As the PLC increased its attacks in Zaire from its sanctuary in the Ugandan Ruwenzori Mountains, Mobutu responded by helping former UPC politicians with close links to Ruwenzururu leaders establish an exile group in Zaire for the purpose of overthrowing the NRM government. Meanwhile, farther north there were intermittent clashes between Ugandan and Zairian soldiers, both as a result of the NRM's campaign to eliminate cross-border smuggling and over fishing rights in the lakes along the border. Large numbers of Ugandans, who had fled into Zaire as refugees during the Amin and second Obote governments, had begun to return to Uganda. But in June 1987, the United Nations High Commissioner for Refugees (UNHCR) program assisting them was closed. And in a bizarre incident that further soured interstate relations, Amin attempted to return to northern Uganda through Zaire in January 1989 but was recognized and held in the airport at Kinshasa. In the absence of an extradition treaty with Uganda, Zaire allowed Amin to return to his home in exile in Saudi Arabia, despite NRM demands for his return to stand trial. In September 1990, Museveni and Mobutu agreed to cooperate in resolving border security problems, but despite this pledge the border area remained unsettled for the rest of the year.

Data as of December 1990