In this study an attempt is made to show how the historical exclusion of Indigenous knowledge (IK) from the policy deliberation process in Canada has had a detrimental impact on Aboriginal peoples in Canada. A definition of the IK paradigm including sources and characteristics is developed, and the nature of the relationship between the marginalized IK paradigm and the dominant European scientific paradigm is examined. A review of the history of Aboriginal peoples in Canada shows how IK came to be marginalized by colonial and Canadian governments, and analyzes how marginalization has contributed to poor social conditions in Aboriginal communities, as well as the deterioration of the governance relationship between Aboriginal peoples and the government of Canada. An argument is developed for the reincorporation of IK into the policy process through the negotiation and implementation of Aboriginal self-government, and evidence is presented showing how self-government would be a more desirable and effective approach to encouraging IK inclusion than reforms to existing consultative and representative institutions.