Recognition of conscientious objection seems reasonable in relation to controversial and contentious issues, such as physician assisted suicide and abortion. However, physicians also advance conscience-based objections to actions and practices that are sanctioned by established norms of medical ethics, and an account of their moral force can be more elusive in such contexts. Several possible ethical justifications for recognizing appeals to conscience in medicine are examined, and it is argued that the most promising one is respect for moral integrity. It is also argued that an appeal to conscience has significant moral weight only if the core ethical values on which it is based correspond to one or more core values in medicine. Finally, several guidelines pertaining to appeals to conscience and their ethical evaluation are presented.