The increasing number of Rwandan refugees in Uganda heightened tensions between Kampala and Kigali throughout the 1980s. The fact that many of these refugees had supported Idi Amin while he was in power provoked official displeasure and retribution during Obote's second presidency. In 1982 Obote, hoping to resolvÍÍÍÍe the refugee problem and prevent challenges to his administration, expelled 60,000 ethnic Rwandans, accusing them of "antigovernment activities." Many of those evicted claimed to be Ugandan citizens whose families had lived in Uganda since the late 1800s.

Museveni, who was of Ankole descent but had relatives in Rwanda, had recruited approximately 1,000 Rwandans into the NRA during the early and mid-1980s. Several journalists had reported that the Rwandans formed the core of the original NRA, and government critics complained about "foreign influence" over the national army. Rumors of Rwandans serving in the Ugandan military forming the Rwandan Patriotic Front (RPF) in the late 1980s alarmed officials in Kigali who believed that the RPF posed a threat to Rwandan president Juvénal Habyarimana. A few officials in Kigali alleged that Museveni had promised assistance to Rwandan insurgents in exchange for their military support in the early 1980s, when he was leading a guerrilla army in western Uganda.

In 1989 Uganda and Rwanda agreed to resolve their differences. In February, for example, Uganda agreed to naturalize a few Rwandans already living in Uganda, while Rwanda pledged to consider repatriating others on a case-by-case basis. In early May, Museveni and Habyarimana affirmed their commitment to resolve the refugee problem with assistance from the UNHCR.

Despite both governments' optimism that these discussions marked the beginning of improved relations, hostilities between the two countries soon resumed. On October 1, 1990, the RPF invaded Rwanda from bases in Uganda. The initial force, numbering a few thousand, grew to approximately 7,000, including roughly 4,000 deserters from the NRA and a number of Rwandan refugees. The RPF issued its Eight-Point Program calling for economic and political reforms in Rwanda, similar to those espoused by Museveni in Uganda.

As the war spread throughout northern Rwanda in late 1990, relations between the two countries became more strained. President Habyarimana repeatedly accused Uganda of providing military assistance to the RPF and preparing to invade Rwanda, charges that Kampala consistently denied. President Museveni, in turn, accused Rwandan government troops of conducting "hot pursuit" operations into Uganda. Repeated efforts to negotiate an end to the fighting in Rwanda failed.

Data as of December 1990