The majority of Christians were found in the south. A few isolated mission stations and mission bookstores, along with churches serving southern enclaves in the northern cities and larger towns, dotted the Muslim north. The Yoruba area traditionally has been Protestant and Anglican, whereas Igboland has always been the area of greatest activity by the Roman Catholic Church. Other denominations abounded as well. Presbyterians arrived in the early twentieth century in the Ibibio Niger Delta area and had missions in the middle belt as well. This latter area was an open one. Small missionary movements were allowed to start up, generally in the 1920s, after the middle belt was considered pacified. Each denomination set up rural networks by providing schooling and health facilities. Most such facilities remained in 1990, although in many cases schools had been taken over by the local state government in order to standardize curricula and indigenize the teaching staff. Pentecostals arrived mostly as indigenous workers in the postindependence period and in 1990 Perte costalism was spreading rapidly throughout the middle belt, having some success in Roman Catholic and Protestant towns of the south as well. There were also breakaway, or Africanized churches that blended traditional Christian symbols with indigenous symbols. Among these was the Aladura movement that was spreading rapidly throughout Yorubaland and into the non-Muslim middle belt areas.

Apart from Benin and Warri, which had come in contact with Christianity through the Portuguese as early as the fifteenth century, most missionaries arrived by sea in the nineteenth century. As with other areas in Africa, Roman Catholics and Anglicans each tended to establish areas of hegemony in southern Nigeria. After World War I, smaller sects such as the Brethren, Seventh Day Adventists, Jehovah's Witnesses, and others worked in interstitial areas, trying not to compete. Although less well-known, African-American churches entered the missionary field in the nineteenth century and created contacts with Nigeria that lasted well into the colonial period.

African churches were founded by small groups breaking off from the European denominations, especially in Yorubaland, where such independence movements started as early as the late nineteenth century. They were for the most part ritually and doctrinally identical to the pavent church, although more African music, and later dance, entered and mixed with the imported church services. A number also used biblical references to support polygyny. With political independence came African priests in both Roman Catholic and Protestant denominations, although ritual and forms of worship were strictly those of the home country of the original missionaries. By the 1980s, however, African music and even dancing were being introduced quietly into church services, albeit altered to fit into rituals of European origin. Southern Christians living in the north, especially in larger cities, had congregations and churches founded as early as the 1920s. Even medium-sized towns (20,000 persons or more) with an establisheafb hed southern enclave had local churches, especially in the middle belt, where both major religions had a strong foothold. The exodus of Igbo from the north in the late 1960s left Roman Catholic churches poorly attended, but by the 1980s adherents were back in even greater numbers, and a number of new churches had been built.

The Aladura, like several other breakaway churches, stress healing and fulfillment of life goals for oneself and one's family. African beliefs that sorcery and witchcraft are malevolent forces against which protection is required are accepted rituals are warm and emotional, stressing personal involvement and acceptance of spirit possession. Theology is biblical, but some sects add costumed processions and some accept polygyny.

Major congregations of the larger Anglican and Roman Catholic missions represented elite families of their respective areas, although each of these churches had members from all levels and many quite humble church buildings. Nevertheless, a wedding in the Anglican cathedral in Lagos was usually a gathering of the elite of the entire country, and of Lagos and Yorubaland in particular. Such families had connections to their churches going back to the nineteenth century and were generally not attracted to the breakaway churches. All major urban centers, all universities, and the new capital of Abuja had areas set aside for the major religions to build mosques and churches and for burial grounds.

Interethnic conflict generally has had a religious element. Riots against Igbo in 1953 and in the 1960s in the north were said to be fired by religious conflict. The riots against Igbo in the north in 1966 were said to have been inspired by radio reports of mistreatment of Muslims in the south. In the 1980s, serious outbreaks between Christians and Muslims occurred in Kafanchan in southern Kaduna State in a border area between the two religions.

Data as of June 1991