The conflict began following the first multi-party elections in the country since its independence from Belgium in 1962, and is seen as formally ending with the swearing-in of President Pierre Nkurunziza in August 2005.

German, and subsequently Belgian, colonial rulers found it convenient to govern through the existing power structure, perpetuating the dominance of the Tutsi minority over the ethnic Hutu majority.

The Belgians generally identified the ethnic distinctions in Burundi and Rwanda with the following observations: the Twa who were short, the Hutu who were of medium height and the Tutsi who were tallest among them.

[9] These elections were immediately preceded by 25 years of Tutsi military regimes, beginning with Michel Micombero, who had led a successful coup in 1966 and replaced the monarchy with a presidential republic.

Instead of helping the problem, these reforms instead served to inflame ethnic tensions as hope grew among the Hutu population that the Tutsi monopoly was at an end.

Though PALIPEHUTU's leadership decided to cooperate with Ndadaye's new government, its military chief commander Kabora Kossan refused to end the insurgency.

The Hutu rebels believed that the coup had proven the impossibility of negotiations, and regarded the new Hutu-dominated civilian government as mere "stooges" of the old regime.

Furthermore, radicals among the Tutsi civil society regarded FRODEBU as génocidaires, believing that the party had initiated the anti-Tutsi mass killings following the 1993 coup.

[14] The Hutu insurgents received support by the neighboring countries of Zaire and Tanzania,[18] both of which allowed the rebels to set up bases on their territories from where they could launch raids into Burundi.

[12][19] The reasons for which they supported the insurgents differed greatly: Zairean President Mobutu Sese Seko believed that he could gain political leverage by harboring Rwandan and Burundian Hutu militants and refugees.

They would suppress anti-Mobutu groups in Zaire, and give him something to bargain with the international community which sought to resolve the Great Lakes refugee crisis.

[20] In contrast, leading Tanzanian statesman Julius Nyerere wanted the region to be stabilized and pacified,[21] and believed that the existence of Burundi and Rwanda as independent states posed a security problem by itself.

[22] In the short term however, Nyerere believed that peace and order could only be achieved in Burundi through the inclusion of Hutus in the Burundian government and military.

[15] These groups included unofficial paramilitary wings of Hutu and Tutsi parties, independent extremist militias, and militant youth gangs.

[2] And despite the CNDD-FDD’s denial of these links, Filip Reyntjens assessed how northern Burundi’s situation made Rwandan and Burundian Hutu rebel groups “objective allies” for geopolitical convenience, given an interest “in effectively controlling this area which could become a major base for an invasion of Rwanda by Rwandan exiles.”[26] This situation, and the decline of state authority in Burundi, greatly alarmed the RPF-led government of Rwanda.

The RPF feared that the collapse of the Burundian government would lead not only to the influx of possibly 500,000 Tutsi refugees into Rwanda, but also provide a new haven to the Rwandan Hutu insurgents.

Rwandan troops would repeatedly cross the border, and attack Hutu refugee camps which harbored rebel forces in coordination with the Burundian military and local Tutsi militias.

[31] The increasing activity of the Hutu rebels in Burundi worried the Rwandan government, and influenced its decision to launch the First Congo War in late 1996 to overthrow President Mobutu of Zaire.

[19] Although Rwanda successfully overthrew Mobutu in a matter of months and replaced him with Laurent-Désiré Kabila, CNDD-FDD rebels still managed to significantly expand their operations in 1997.

[15] In fact, at least elements of the new Congolese government under Laurent-Désiré's son Joseph Kabila came to support the Burundian insurgents by the early 2000s just as Mobutu had done it previously.

He and other heads of states in the region increased the pressure on Burundi's political leadership, pushing them to accept a government with participation of the rebel groups.

[38] After bitter negotiations, an agreement was finally reached which established a transitional government, where the presidency and vice-presidency would be rotated every 18 months, sharing power between the Hutus and Tutsis.

[39] A group of extremist Tutsis also attempted to revive the "Puissance Auto-défense-Amasekanya" (PA-Amasekanya) ethnic militia in mid-2000 to resist the peace agreement, but the leaders of this faction were promptly jailed.

In contrast to earlier attempts to ensure peace which had been sabotaged by army extremists, most of the military had become wary of the constant civil war by the early 2000s.

[citation needed] Confronted by the newly unified Burundian military and the international peacekeepers, as well as a war-wary population, the abilities of the FNL to wage an insurgency gradually whittled down.

[45] In August 2004, the FNL claimed responsibility for killing 160 Congolese Tutsi refugees in a United Nations camp at Gatumba near the Congo border in Burundi.

[45] The attack was strongly condemned by the U.N. Security Council, which issued a statement of outrage at the fact that "most of the victims were women, children and babies who were shot dead and burned in their shelters".

The president signed a law in January 2005 to initiate a new national army, consisting of Tutsi military forces and all but one of the Hutu rebel groups.

Matters continued to look promising after Burundi's last rebel group, the FNL, signed a ceasefire deal in Tanzania, "solidifying the end of a 12-year civil war."

[8]In 2014 the Truth and Reconciliation Commission (TRC) was established to investigate crimes committed during ethnic violence since independence in 1962, overseen by Pierre Claver Ndayicariye.