Conscience rights have become contentious in modern healthcare. Examples abound of legally permitted but morally controversial procedures, where local rulings seek to force clinicians to perform such actions. Yet most healthcare professionals want to exercise their own judgment in deciding whether to participate. For many, this is a line in the sand, and “conscience is said to be supreme.” Wesley Smith claims there will soon be “medical martyrs,” who have stuck to their principles and have been stripped of their credentials. Much of this is based on moral complicity, the idea that an agent may be morally culpable for the immoral acts actually performed by another agent. Classically, complicity may occur in two ways. Formal complicity is where two actors share the same evil intent, and the one directly facilitates the actions of the other. Such cooperation with evil is always ethically forbidden. Material complicity, on the other hand, is more indirect, where the two actors are separated by time, knowledge, or intent. Such complicity may or may not be immoral. To the busy clinician, all this may seem vague and theoretical. This paper will examine the concept of moral complicity, presenting practical guidelines for healthcare practitioners during a crisis of conscience. The goal is to balance fiduciary duties and patient autonomy against the clinician’s personal convictions, to help him or her to know when to refuse, when to refer, and when to go along with a practice.