Conscience is an idea that has significant currency in liberal democratic societies. Yet contemporary moral philosophical scholarship on conscience is surprisingly sparse. This paper seeks to offer a rigorous philosophical account of the role of conscience in moral life with a view to informing debates about the ethics of conscientious objection in medicine. I argue that conscience is concerned with a commitment to moral integrity and that restrictions on freedom of conscience prevent agents from living a moral life. In section (...) one I argue that conscience is a principle of moral awareness in rational agents, and that it yields an awareness of the personal nature of moral obligation. Conscience also monitors the coherence between an agent’s identity-conferring beliefs and intentions and their practical actions. In section two I consider how human beings are harmed when they are forced to violate their conscience. Restrictions on the exercise of conscience prevent people from living in accord with their own considered understanding of the requirements of morality and undermine one’s capacity for moral agency. This article concludes with a consideration of how a robust theory of conscience can inform our understanding of conscientious objection in medicine. I argue that it is in the interest of individual practitioners and the medical profession generally to foster moral agency among doctors. This provides a prima facie justification for permitting at least some kinds of conscientious objection. (shrink)