Military physicians are often perceived to be in a position of ‘dual loyalty’ because they have responsibilities towards their patients but also towards their employer, the military institution. Further, they have to ascribe to and are bound by two distinct codes of ethics (i.e., medical and military), each with its own set of values and duties, that could at first glance be considered to be very different or even incompatible. How, then, can military physicians reconcile these two codes of ethics and their distinct professional/institutional values, and assume their responsibilities towards both their patients and the military institution? To clarify this situation, and to show how such a reconciliation might be possible, we compared the history and content of two national professional codes of ethics: the Defence Ethics of the Canadian Armed Forces and the Code of Ethics of the Canadian Medical Association. Interestingly, even if the medical code is more focused on duties and responsibility while the military code is more focused on core values and is supported by a comprehensive ethical training program, they also have many elements in common. Further, both are based on the same core values of loyalty and integrity, and they are broad in scope but are relatively flexible in application. While there are still important sources of tension between and limits within these two codes of ethics, there are fewer differences than may appear at first glance because the core values and principles of military and medical ethics are not so different.