The literature on conscience in medicine has paid little attention to what is meant by the word ‘conscience.’ This article distinguishes between retrospective and prospective conscience, distinguishes synderesis from conscience, and argues against intuitionist views of conscience. Conscience is defined as having two interrelated parts: (1) a commitment to morality itself; to acting and choosing morally according to the best of one’s ability, and (2) the activity of judging that an act one has done or about which one is deliberating (...) would violate that commitment. Tolerance is defined as mutual respect for conscience. A set of boundary conditions for justifiable respect for conscientious objection in medicine is proposed. (shrink)