In the 16th century, Burundi was a kingdom characterized by a hierarchical political authority and tributary economic exchange. A king (mwani) headed a princely aristocracy (ganwa) which owned most of the land and required a tribute, or tax, from local farmers and herders. In the mid-18th century, this Tutsi royalty consolidated authority over land, production, and distribution with the development of the ubugabire--a patron-client relationship in which the populace received royal protection in exchange for tribute and land tenure.

Although European explorers and missionaries made brief visits to the area as early as 1856, it was not until 1899 that Burundi came under German East African administration. In 1916 Belgian troops occupied the area. In 1923, the League of Nations mandated to Belgium the territory of Ruanda-Urundi, encompassing modern-day Rwanda and Burundi. The Belgians administered the territory through indirect rule, building on the Tutsi-dominated aristocratic hierarchy. Following World War II, Ruanda-Urundi became a United Nations Trust Territory under Belgian administrative authority. After 1948, Belgium permitted the emergence of competing political parties. Two political parties emerged: the Union for National Progress (UPRONA), a multi-ethnic party led by Tutsi Prince Louis Rwagasore and the Christian Democratic Party (PDC) supported by Belgium. In 1961, Prince Rwagasore was assassinated following an UPRONA victory in legislative elections.

Full independence was achieved on July 1, 1962. In the context of weak democratic institutions at independence, Tutsi King Mwambutsa IV established a constitutional monarchy comprising equal numbers of Hutus and Tutsis. The 1965 assassination of the Hutu prime minister set in motion a series of destabilizing Hutu revolts and subsequent governmental repression. In 1966, King Mwambutsa was deposed by his son, Prince Ntare IV, who himself was deposed the same year by a military coup lead by Capt. Michel Micombero. Micombero abolished the monarchy and declared a republic, although a de facto military regime emerged. In 1972, an aborted Hutu rebellion triggered the flight of hundreds of thousands of Burundians. Civil unrest continued throughout the late 1960s and early 1970s.

In 1976, Col. Jean-Baptiste Bagaza took power in a bloodless coup. Although Bagaza led a Tutsi-dominated military regime, he encouraged land reform, electoral reform, and national reconciliation. In 1981, a new Constitution was promulgated. In 1984, Bagaza was elected head of state, as the sole candidate. After his election, Bagaza's human rights record deteriorated as he suppressed religious activities and detained political opposition members.

In 1987, Maj. Pierre Buyoya overthrew Colonel Bagaza. He dissolved opposition parties, suspended the 1981 constitution, and instituted his ruling Military Committee for National Salvation (CSMN). During 1988, increasing tensions between the ruling Tutsis and the majority Hutus resulted in violent confrontations between the army, the Hutu opposition, and Tutsi hardliners. During this period, an estimated 150,000 people were killed, with tens of thousands of refugees flowing to neighboring countries. Buyoya formed a commission to investigate the causes of the 1988 unrest and to develop a charter for democratic reform.

In 1991, Buyoya approved a Constitution that provided for a president, multi-ethnic government, and a parliament. Burundi's first Hutu president, Melchior Ndadaye, of the Hutu-dominated FRODEBU Party, was elected in 1993. He was assassinated by factions of the Tutsi-dominated armed forces in October 1993. The country was then plunged into civil war, which killed tens of thousands of people and displaced hundreds of thousands by the time the FRODEBU government regained control and elected Cyprien Ntaryamira president in January 1994. Nonetheless, the security situation continued to deteriorate. In April 1994, President Ntayamira and Rwandan President Juvenal Habyarimana died in a plane crash. This act marked the beginning of the Rwandan genocide, while in Burundi, the death of Ntaryamira exacerbated the violence and unrest. Sylvestre Ntibantunganya was installed as president for a 4-year term on April 8, but the security situation further deteriorated. The influx of hundreds of thousands of Rwandan refugees and the activities of armed Hutu and Tutsi groups further destabilized the regime.