The Global War on Terrorism brings significant ethical challenges for military physicians. From Abu Ghraib to Guantanamo Bay, the actions of health care providers have come under considerable scrutiny. Military providers have dual roles as military officers and medical professionals, which have the potential to come into conflict. Often they are inadequately prepared to manage this conflict. We review pertinent historical precedents, applicable laws, ethical guidelines, and military regulations. We also present examples of ethical challenges deployed clinicians have faced and their ethical solution. Finally, we propose a practical strategy to educate physicians on how to manage complex ethical dilemmas in war time settings.