The church in Uganda was born in martyrdom. The arrival of the Englishmen, Speke and Grant, in 1862 opened the Bugandan kingdom to outside influences, including Islam missionaries from Zanzibar. H.M. Stanley arrived in 1875 and initiated the sending of missionaries by the Church Missionary Society. A party of 8 missionaries was sent to Buganda in 1876, but through death and illness only 2, Smith and Wilson, reached Uganda the following year. Later the same year Smith died. Wilson was joined in 1878 by Alexander Mackay, who became the father of the gospel in Uganda - teacher, builder, evangelist, printer and pastor. Soon after Mackay’s arrival, Roman Catholic missionaries also came to the court of the kabaka, Mutesa, the Ugandan ruler. They were French White Fathers, committed to the evangelisation of Equatorial Africa.

The differences between Protestant and Catholic missions left Mutesa puzzled. He flirted with both missions, and the existence of pagan, Moslem, Protestant, and Catholic traditions provided a setting for considerable conflict. Nevertheless, Mackay made some progress. When Mutesa died in 1884, his son Mwanga, then only 18 became ruler, but while his father had played-off the three religions, Catholics, Protestants and Muslims, against each other and thus balanced the influence of the European colonial powers that were backing each group. Mwanga took a much more aggressive approach, expelling missionaries and insisting that Christian converts abandon their faith or face death. This resulted in the deaths of about 30 of the pages at the court. Anglicans and Roman Catholics were slowly burned alive together on 31 January 1885.

The gospel continued to spread however. In October 1885, Bishop Hannington, sent out as the first bishop of Eastern Equatorial Africa, was assassinated at the border on Mwanga's orders. There followed the most horrific period in the story of the Christian faith in Uganda. Some of Mwanga’s pages had become Christian and been baptised. Mwanga, made sexual advances, towards these boys and he considered their refusal to be insolent disobedience that threatened his absolute authority, he blamed their Christian faith. In May 1886 he set out to destroy both Protestants and Catholics. 32, mainly young Christians at the court of Mwanga, were killed, and many others died in the months of persecution that followed.

Mwanga’s rage was directed at Christian converts from his own people. Mackay and the Roman Catholics continued their work, quietly, away from the court. The situation in Buganda eventually degenerated into civil war, from which order emerged only in the 1890s. At the same time began the great missionary work of Apolo Kivebulaya building on the foundations of the martyrs of Uganda. Today the martyrs, Anglican and Roman Catholic, are commemorated together. The known victims include Joseph Mkasa, who protested the murder of Bishop Hannington, Charles Lwanga, a court official who had baptised some of the pages and tried to protect them from Mwanga, Andrew Kagwa a catechist, and Matthias Murumba, a judge.