The majority of Burundians are Christian: about 60% are Roman Catholic and 5% are Protestants. About 1% are Muslims and the rest practice traditional indigenous beliefs. Current laws allow freedom of worship for all.

The early German and Belgian missionaries introduced Christianity to Burundi. Missionaries not only converted people to Christianity, but also gave them a European-style education. Today, Christianity is still the dominant religion, but people in rural areas, where there are few churches, often cannot attend church regularly. In some rural areas, priests perform weddings at the home of the bride or groom, because there is no church nearby.

Many Burundians, including most of the Twa people and some Christian Burundians, maintain indigenous beliefs which include forms of animism. Animists believe that inanimate and natural phenomena, as well as living creatures, have souls and spirits. Imana is the creator of the universe and source of all good. When people die, their spirits are honoured and referred to as imizimu. Certain rituals are believed to control uncertainties and negative influences in life. This can be achieved by harnessing positive forces from ancestors or other spirits and by limiting negative forces.

Animist rituals may be performed to cure a person who is ill, to prevent a drought or a flood, to obtain a good harvest or to ensure good luck for a newly married couple. The kubandwa is performed to exorcise bad spirits which cause problems and to invoke good spirits to help solve a problem. During the ceremony, participants shake an inyagara (a rattle made from a calabash gourd).

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In indigenous religions, a kiranga (priest) acts as an intermediary between the god Imana and humans. Persons seeking help from Imana will ask the kiranga to intercede with the god on their behalf. An offering which may be in the form of food, drink or other gifts is made to the kiranga.