Increasingly, physicians are being asked to provide technical services that many believe are morally wrong or inconsistent with their beliefs about the meaning and purposes of medicine. This controversy has sparked persistent debate over whether practitioners should be permitted to decline participation in a variety of legal practices, most notably physician-assisted suicide and abortion. These debates have become heavily politicized, and some of the key words and phrases are being used without a clear understanding of their meaning. In this essay, I endeavor, firstly, to clarify the meaning of some of these terms: conscience, conscientious action, professional judgment, conscientious objection, conscience clauses, civil disobedience, and tolerance. I argue that use of the term conscientious objection to describe these refusals by health care professionals is mistaken and confusing. Secondly, relying on a proper understanding of the moral and technical character of medical judgment, the optimal deference that the state and markets ought to have toward professions, and general principles of Lockean tolerance for a diversity of practices and persons in a flourishing, pluralistic, democratic society, I offer a defense of tolerance with respect to the deeply held convictions of physicians and other health care professionals who hold minority views on contested but legal medical practices.