The accession to power of the National Resistance Movement in Uganda in 1986 was intended to inaugurate a new beginning for Uganda, an end to the political, ethnic and religious divisions that had characterised the country's violent history since the 1960s. Although peace, stability and the strengthening of democratic structures have brought substantial progress to many parts of the country, the Acholi of Northern Uganda have felt largely excluded from these benefits. Violence and insecurity have characterised the districts of Gulu and Kitgum since 1986. It is not simply the failure of development that has been so distressing for the inhabitants, but the collapse of the moral framework and the institutions that gave society coherence. Religion has played a considerable part in articulating the sense of loss and anger at this state of affairs. Traditional Acholi and Christian religious sentiments have helped to shape and sustain rebel movements against the central government, and to inform Acholi responses to the violence inflicted by rebels and government. The article, based on field work conducted in 1999, examines ways in which the main Churches, Catholic and Protestant (Anglican), have historically been bound up with the political divisions of Acholi. It examines the painful adjustments which loss of access to power has necessitated, particularly for the Anglican Church. Since 1986 the Churches have had a vital role in conflict resolution and in envisioning new futures for Acholi. The majority of the population, required to live in 'protected villages', have few material and spiritual resources. The importance of Christian faith and practice for Acholi living in such situations of prolonged conflict, with few signs of speedy resolution, is assessed.