What role should the physician's conscience play in the practice of medicine? Much controversy has surrounded the question, yet little attention has been paid to the possibility that disputants are operating with contrasting definitions of the conscience. To illustrate this divergence, we contrast definitions stemming from Abrahamic religions and those stemming from secular moral tradition. Clear differences emerge regarding what the term conscience conveys, how the conscience should be informed, and what the consequences are for violating one's conscience. Importantly, these basic disagreements underlie current controversies regarding the role of the clinician's conscience in the practice of medicine. Consequently participants in ongoing debates would do well to specify their definitions of the conscience and the reasons for and implications of those definitions. This specification would allow participants to advance a more philosophically and theologically robust conversation about the means and ends of medicine.