Burundian Civil War The Burundian Civil War was an armed conflict lasting from 1993 to 2005 . The civil war was the result of long standing ethnic divisions between the Hutu and the Tutsi tribes in Burundi . The conflict began following the first multi - party elections in the country since independence from Belgium in 1962 , and is seen as formally ending with the swearing in of Pierre Nkurunziza in August 2005 . The estimated death toll stands at 300 , 000 killed . Background . The origins of Tutsi and Hutu as distinct ethnic groups is unclear , but became the basis of a society organized under colonial racial schemes . In the case of the Belgians , and the Germans before them , casual observations revealed varying height differences among the resident peoples : the Twa who were short , the Hutu who were of medium height and the Tutsi who were tallest among them . It was also documented that in many cases , those who were among the tall group also raised cattle and tended to be politically and economically dominant . Those in the middle height group , on the other hand , tended to be poor and more agrarian . This prompted the use of what became known as the " ten - cow " rule . Those individuals who owned more than ten cows were described as " well - born , " equated with Caucasians , and given privileges by the colonists . The ten - cow rule was not universally applied , however , and the existence of " petits Tutsi " continues to cause much debate in the field . This much is clear , the Belgian census of 1933 - 34 and subsequent division of " races " exacerbated latent regional and ethnic conflicts . When anti - colonialism swept across Africa and agitation began for independence , Belgium bolted from the colonies in a hurry . Declaring an intention not to shed blood to hold to their colonies , the Belgians declared " pas un seul soldat pour Afrique " ( not a single soldier for Africa ) Federation with Rwanda was rejected , and Rwanda and Burundi separated . Rwanda underwent its " Social Revolution " , became a republic and Hutus killed Tutsis . Burundi chose to retain its monarchy . Burundi ’ s first multi - party national elections were held on 27 June 1993 . 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 . The last of the coups was in 1987 and installed Tutsi officer Pierre Buyoya . Buyoya attempted to institute a number of reforms to ease state control over media and attempted to facilitate a national dialogue . Instead of helping the problem , these reforms instead served to inflame ethnic tensions as hope grew amongst the Hutu population that the Tutsi monopoly was at an end . Local revolts subsequently took place by Hutu peasants against several Tutsi leaders in northern Burundi ; these Hutu militias killed hundreds of Tutsi families in the process . When Buyoya sent in the army to quell the uprising , they in turn killed thousands of Hutu . War . On October 21 , 1993 , Burundi ' s first democratically elected Hutu president , Melchior Ndadaye , was assassinated by Tutsi extremists . As a result of the murder , violence broke out between the two groups , and an estimated 50 , 000 to 100 , 000 people died within a year . A 1996 UN report into Ndadaye ' s assassination and its aftermath , concluded that " acts of genocide against the Tutsi minority were committed in Burundi in October 1993 " . The report also implicated senior figures in Burundi ' s Tutsi - dominated army in the assassination . In Burundi , Tutsi civilians have been targets of mass killings and acts of genocide organized by the state and by armed militia groups ( see Burundi genocide ( 1993 ) ) . They were followed by a long civil war that killed both Hutu and Tutsi . This violence prompted Buyoya to speed up liberalization and national dialogue , allowing other political parties to compete in the 1993 election . Melchior Ndadaye was democratically elected and became first Hutu president in the country ’ s history . He was assassinated three months later , in October 1993 , by Tutsi army extremists . The country ’ s situation rapidly declined as Hutu peasants began to rise up and massacre Tutsi . In acts of brutal retribution , the Tutsi army proceeded to round up thousands of Hutu and kill them . The Rwandan Genocide in 1994 , sparked by the killing of Ndadaye ’ s successor Cyprien Ntaryamira , further aggravated the conflict in Burundi by sparking additional massacres of Tutsis . Assassination of Ntaryamira . In 1994 , Ndadaye ’ s successor Cyprien Ntaryamira was assassinated in the same plane crash with Rwandan President Juvenal Habyarimana . This act marked the beginning of the Rwandan Genocide , while in Burundi , the death of Ntaryamira exacerbated the violence and unrest , although there was no general massacre . Sylvestre Ntibantunganya was installed to a 4 - year presidency on April 8 , but the security situation further declined . The influx of hundreds of thousands of Rwandan refugees and the activities of armed Hutu and Tutsi groups further destabilized the regime . After the assassination of Ntaryamira the Hutu presidency and Tutsi military operated under a power - sharing political system until 1996 , when Tutsi Pierre Buyoya replaced the Hutu president in a coup . Hutu rebels killed about 300 Tutsis on July 20 , 1996 , and army soldiers killed at least 126 Hutu refugees on January 5 , 1997 . In 1998 , Buyoya and the opposition - led Hutu parliament reached an agreement to sign a transitional constitution , and Buyoya was sworn in as president . The Arusha peace talks began on 15 June 1998 . The civil war , however , continued , despite the efforts of the international community to create a peace process . Ceasefire talks were held in Tanzania in 2000 , facilitated by Nelson Mandela . The agreement which established a transitional government , where the presidency and vice - presidency would be rotated every 18 months , sharing power between the Hutus and Tutsis was reached . While the government and three Tutsi groups signed the ceasefire accord , two leading Hutu rebel groups refused to participate , and the fighting continued . The Arusha talks closed with little progress made on November 30 , 2000 . 20 Tutsis and one British woman were killed on 28 December 2000 , in the Titanic Express massacre . On 18 April 2001 , an attempted coup failed . The transitional government was implemented in October 2001 . 300 boys were kidnapped from Museuma College on November 9 , 2001 . Main Hutu rebel groups had still refused to sign a ceasefire agreement at this time , and 500 rebels were killed in their own attack against the Tutsi army on December 25 , 2001 . This resulted in increased fighting for several months . The 9 September 2002 Itaba massacre left hundreds of unarmed civilians dead . Presidency of Ndayizeye . On 9 April 2003 , the force headquarters of the African Union Mission in Burundi was established in Bujumbura under South African Major General Sipho Binda . On 18 October 2003 , it was announced that the mission had reached full strength : 1 , 483 South Africans , 820 Ethiopians , and 232 personnel from Mozambique . In July 2003 , a rebel attack on Bujumbura left 300 dead and 15 , 000 displaced . Also in July , Domitien Ndayizeye , a Hutu , took over as president of the transitional government , and Buyoya stepped down . Along with the main Hutu rebel group , National Council for the Defense of Democracy – Forces for the Defense of Democracy ( FDD ) , President Ndayizeye signed a ceasefire agreement at a summit of African leaders in Tanzania in November 2003 . Under the agreement , the FDD became a political party , and it was decided that rebel Hutu fights were to be integrated into the predominately Tutsi armed forces . On December 29 , 2003 , Archbishop Michael Courtney , the " papal nuncio " for the country , was murdered . Disaster occurred in 2004 when the Hutu rebel group , Forces of National Liberation ( FNL ) , claimed responsibility for killing 160 Congolese Tutsi refugees in a United Nations camp at Gatumba near the Congo border in Burundi . 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 Council called on the top U . N . envoy in Burundi to investigate the incident with a U . N . representative from Congo , a step that increased U . N . intervention in the Burundi civil war . A few months later in December , U . N . and government forces began to disarm thousands of Burundi soldiers and former rebels . Peace process . In 2005 , many developments were made in the peace process . The president signed a law in January 2005 to initiate a new national army , consisting of Tutsi military forces and all but one Hutu rebel groups . The Constitution was approved by voters in a referendum — marking the first time for Burundians to vote since 1994 . They voted again in the July during the parliamentary elections , postponed from November 2004 , in which " the Government of Burundi and the Independent National Electoral Commission conducted a sound election , carried out in an atmosphere of peace and security . " The FDD ended up being the winning party for the parliamentary elections . Several months later , Pierre Nkurunziza , from the Hutu FDD group , was elected as president by the two Hutu - dominated houses of parliament . After 12 years of living with a midnight - to - dawn curfew , Burundians were free to stay out late when the curfew was lifted on April 15 , 2006 , for the first time since 1993 . This signified the most stable point in Burundi civil affairs since the assassination of Hutu President Melchior Ndadaye and the beginning of the civil war . Matters continued to look prosperous after Burundi ’ s last rebel group , the Forces of National Liberation ( FNL ) signed a ceasefire deal in Tanzania , " solidifying the end of a 12 - year civil war . " As part of the agreement , members of the FNL were to be assembled , demobilized , and integrated into the national army . In mid - April 2008 , FNL rebels shelled the capital , Bujumbura , while fighting killed at least 33 .