This article explores the role of emotion and alienation in protracted conflict and makes suggestions as to how they might be managed. First we note the scant attention given to these topics in the mediation and negotiation literature. Then we show how emotional and relational issues are related to theories of economic and political interests, on the one hand, and narratives and ideologies of conflict, on the other. We focus on the way alienated relationships impair communication and the way they generate intense emotions, especially shame and anger. In our view, secret (unacknowledged) alienation and shame are the primary causes of intractable conflict. Finally, we propose a role for mediators in the acknowledgment of emotion and alienation as a way of resolving intractable conflicts.