Kiwanuka was a Muganda of Buffalo (Mbogo) Clan originating from Ssenge in Busiro County. His father was Bunga who had many wives and about one hundred children. Of these, seventy four survived forty one boys and thirty three girls. His mother was Kasswa of the Monkey clan.
Kiwanuka was born at Minziiro at the boundary of Tanzania and Uganda. He was brought up at Kakuuto near Bigada Parish.
It was Bigomba an official in the private apartment if the King who took Kiwanuka to the People of King Muteesa I. Bigomba was in charge of the intelligence department.
The boy worked as page. Kiwanuka was exceptionally intelligent, when he took up the catholic instructions; it took him only three days to learn all the prayers and the whole catechism in four months.
Muzeyi had an exceptional devotion and knowledge in the traditional medicine of various diseases. Though not official, John Mary Kiwanuka Muzeyi could be considered the first Uganda religious brother.