At the end of the 19th century, the new Christian religion had made an impact in Uganda, clashing with the traditional religions. The Kabaka (King of the Baganda), refused to let people convert to Christianity because he wanted the people to worship him, and the Christians in his court refused his homosexual advances. The Christian boys in the court stood firm in their faith. They were wrapped in wet mats and roasted alive in a fire. These boys and others who were killed by the Kabaka are honored as martyrs in Uganda, and there is a shrine built to them, and a national holiday. Because of the “worship” of these martyrs by Catholic churches, many evangelicals have stopped remembering them altogether. Two ditches Christians fall into.
The next period of persecution was under Idi Amin, who outlawed all the evangelical churches and killed many of the Christians. He technically permitted the Anglican and Roman Catholic churches, but when the Archbishop of the Church of Uganda spoke against him, he personally beat him to death. Under Amin the jails were full of Christians, but the jails were converted into churches.
The situation today is no longer one of persecution, actually it is the opposite- it is trendy to be a Christian. The problem in Kampala is the “prosperity gospel” – pastors basically advertise their church saying “come and you will have big cars and lots of money and go to America.” This is in the cities, in the villages there are many faithful pastors. So you can’t generalize, but the main problem today is that people who “convert” are more concerned with what they can get from Christianity than what they can give- their lives.
Christianity in Uganda is being shaken, and the false doctrines being shown for what they are. Until recently there were “big men” or “prophets” who ruled churches in fear because they could actually make people die or their ministry fall apart if they opposed them. Christians, including Uncle Jonnes, prayed that God would show who was greater, Himself or one of these men, and the man jumped out a window and killed himself for no reason one day.

