Informed consent in military research shares many of the same fundamental principles and regulations that govern civilian biomedical research. In fact, much of modern research ethics is grounded in events that occurred in the context of war or government-sponsored research. Despite these similarities and common origins, research in the military has additional requirements designed to preserve service members' informed consent rights. The special nature of the superior-subordinate relationship in the military necessitates careful protections to avoid perceptions of coercion or undue influence on a military subject. Additionally, current legal and regulatory requirements for advanced informed consent significantly restrict the flexibility of the military to conduct research using waiver of consent. This has implications on the ability of the nation to develop effective medical treatments for the global war on terrorism. Nevertheless, work is under way to realign defense research policy with the norms of civilian biomedical practice. Future directions include the adoption of waivers for military emergency research, and the cautious introduction of human subject studies on the battlefield. This paper discusses historical background, regulatory differences, and concerns and challenges of some of these regulatory differences for research personnel that apply to informed consent and waiver of said informed consent for emergency research conducted by the U.S. military.