This study investigates the complications raised in teaching a confessional Religious Education in a multi-religious context pertaining in Ugandan religiously founded public schools, government and private founded schools. The thesis contends that the introduction of Islam, Anglican and Roman Catholic Christian religious traditions in Uganda not only presented alternative religious systems to the existing African traditional religion but ushered in an era of competition for converts that subsequently led to religious conflict. The thesis also submits the view that the missionary aim of formal education in Uganda led to the creation, not only of a denominational, but a divisive educational system. While the study commends the colonial government and the first independent government's efforts towards establishing a nondenominational educational system, it suggests that their failure to address the controversial questions raised by the nature of RE at the time was a missed opportunity. The study probes the current syllabuses, aims and content of CRE and IRE for secondary and primary schools and suggests that their main intention of promoting spiritual growth of students is inappropriate for implementation in the multi-religious schools. The thesis questions the government's proposed exclusion of RE from the education curriculum and its replacement with Moral Education. It suggests that while Moral Education could be a subject on its own, Religious Education needs to be maintained but re-designed to address the multi-religious context. It presents a multi-faith RE as the ideal format of teaching about religion.