In the election the Hutu won a majority however King Mwambutsa refused to appoint the Hutu leader Gervais Nyangoma as Prime Minister instead appointing his former personal secretary, Léopold Biha, a Tutsi, to the role. On October 18th that year Gervais Nyangoma, launched a coup against the king which triggered a massacre by the largely Hutu police force of Tutsis in some parts of the country.

The coup failed and order was restored with Mwambutsa still king, however there were brutal Tutsi retaliations with thousands of ordinary Hutu as well as their political leaders being shot. In 1966 Mwambutsa IV was deposed by his son Ntaré V who appointed the Secretary of Defence Michel Micombero, who had crushed the uprising against his father, as prime minister.

However, within months on 28th November 1966, Micombero staged a military coup and installed himself as president. There followed twenty five years of Tutsi military rule much to the resentment of the Hutu population as only 15% of Burundians are Tutsi with the remaining being of Hutu ethnicity. This period saw a series of military coups and civil insurections leaving hundreds of thousands of Hutu dead, however at the end of this period, following another coup by Maj. Pierre Buyoya, reforms were instigated to help heal the country's ethnic divisions and elections called.

Ironically this easing of state control only served to inflame ethnic tensions as they raised expectations of an end to Tutsi minority control of the country and there were revolts, particularly in the north of Burundi against Tutsi leaders in which hundreds of Tutsi families were killed. Buyoya responded by sending in the army and thousands of Hutu were killed.

Despite this, Buyoya continued with his liberalising reforms and allowed multi party elections in 1993, an election which saw Burundi's first ever democratically elected president, Melchior Ndadaye, a Hutu and both former leader of the 'Mouvement des Étudiants Progressistes Barundi au Rwanda', (a movement of exiled Burundian students) and a founding father of the Burundi Workers' Party, take office on July 10th 1993.

Ndadaye established a pro Hutu government however appointed Sylvie Kinigi, a female Tutsi (though married to a Hutu), as the Prime Minister in an act of conciliation. His presidency though was to be short lived as he was assassinated along with six of his ministers just over three months later on 21st October 1993 during a failed military coup by disgruntled Tutsi members of the armed forces. In response, the Hutu rose in their masses and started slaughtering Tutsis.

Cyprien Ntaryamira, the Minister for Agriculture and a Hutu, was selected as Ndadaye's successor on 5th February 1994 in the hope that his moderate views would ease the violence ravaging the country, however just two months later on 6th April 1994, he was assassinated along with Rwandan president Juvénal Habyarimana when his plane was shot down as it came in to land at Kigali airport in Rwanda. The Burundi civil war then broke out in earnest, with an estimated 300,000 dead between 1993 and the end of the civil war in 2005.

Even children were forced to participate in the bloodshed under pain of death. The UN intervened following an atrocity claimed by the (Hutu) Forces of National Liberation (FNL) in 1994 when they murdered hundreds of Tutsis in a UN run refugee camp.

An uneasy peace was struck and the war drew to a close in 2005, with former Hutu rebel leader Pierre Nkurunziza being elected president by Parliament although some claim 2008 as it was in that year that FNL fighters shelled the capital of Burundi, Bujumbura, killing at least thirty three people.