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An estimated 25% of the population holds traditional indigenous beliefs (animism), which are prevalent in rural areas throughout the country. Some animists have been baptized but do not identify themselves as Christians, or they combine Christian and animist practices.

An estimated 25% of the population holds traditional indigenous beliefs (animism), which are prevalent in rural areas throughout the country. Some animists have been baptized but do not identify themselves as Christians, or they combine Christian and animist practices.

Christians are the third largest religious group, traditionally concentrated in the south and the Nuba Mountains. Widespread displacement and migration during the long civil war increased the population of Christians living in the north. While many Christians have returned to the south, Khartoum still has a significant Christian population. The Roman Catholic Church of Sudan and the Episcopal Churches of Sudan estimate they have six million and five million baptized followers, respectively, although active churchgoers are far fewer.

Christians are the third largest religious group, traditionally concentrated in the south and the Nuba Mountains now located mostly in [[South Sudan]]. Widespread displacement and migration during the long civil war increased the population of Christians living in the north. While many Christians have returned to the south, Khartoum still has a significant Christian population. The Roman Catholic Church of Sudan and the Episcopal Churches of Sudan estimate they have six million and five million baptized followers, respectively, although active churchgoers are far fewer and many followers have fled to [[South Sudan]].

There are very small but long-established groups of Orthodox Christians in Khartoum and other northern cities, including Coptic Orthodox and Greek Orthodox. There are also Ethiopian and Eritrean Orthodox communities in Khartoum and the east, largely made up of refugees and migrants. Other Christian groups with smaller followings include the Africa Inland Church, Armenian (Apostolic) Church, Sudan Church of Christ, Sudan Interior Church, Jehovah's Witnesses, Sudan Pentecostal Church, Sudan Evangelical Presbyterian Church (in the north), Presbyterian Church of the Sudan (in the south), and the Seventh-day Adventist Church of Sudan.

There are very small but long-established groups of Orthodox Christians in Khartoum and other northern cities, including Coptic Orthodox and Greek Orthodox. There are also Ethiopian and Eritrean Orthodox communities in Khartoum and the east, largely made up of refugees and migrants. Other Christian groups with smaller followings include the Africa Inland Church, Armenian (Apostolic) Church, Sudan Church of Christ, Sudan Interior Church, Jehovah's Witnesses, Sudan Pentecostal Church, Sudan Evangelical Presbyterian Church (in the north), Presbyterian Church of the Sudan (in the south), and the Seventh-day Adventist Church of Sudan. Since 2011 many them have fled to [[South Sudan]].

Religion plays a prominent role in the complex system of political alliances. Northern Muslims have dominated the political and economic system since independence in 1956. Since the signing of the Comprehensive Peace Agreement (CPA) in 2005, the GNU has appointed both Muslims and Christians to prominent executive positions.

Religion plays a prominent role in the complex system of political alliances. Northern Muslims have dominated the political and economic system since independence in 1956. Since the signing of the Comprehensive Peace Agreement (CPA) in 2005, the GNU has appointed both Muslims and Christians to prominent executive positions.