Human development and security in the Great Lakes Region (GLR) of Africa have been threatened in the recent past by civil strife. The democratization process in Africa has again brought to the fore the phenomenon of ethnicity and, even in Uganda where the democratization process has been attempted along ‘innovative lines’, human development may ultimately be threatened by ethnicity as a political force. Therefore, this chapter aims to examine the nature of the ethnic crisis in the GLR and in particular its effect on governance in Uganda, noting that changes in the global system have had diverse impacts on the country’s political, economic and social relations.