This paper interprets the relation between sovereignty and guilt in Nietzsche's Genealogy. I argue that, contrary to received opinion, Nietzsche was not opposed to the moral concept of guilt. I analyse Nietzsche's account of the emergence of the guilty conscience out of a pre-moral bad conscience. Drawing attention to Nietzsche's references to many different forms of conscience and analogizing to his account of punishment, I propose that we distinguish between the enduring and the fluid elements of a ‘conscience’, defining the enduring element as the practice of forming self-conceptions. I show that for Nietzsche, the moralization of the bad conscience results from mixing it with the material concepts of guilt and duty, a process effected by prehistoric religious institutions by way of the concept of god. This moralization furnishes a new conception of oneself as a responsible agent and holds the promise of sovereignty by giving us a freedom unknown to other creatures, but at the price of our becoming subject to moral guilt. According to Nietzsche, however, the very forces that made it possible have spoiled this promise and, under the pressures of the ascetic ideal, a harmful notion of responsibility understood in terms of sin now dominates our lives. Thus, to fully realize our sovereignty, we must liberate ourselves from this sinful conscience.