The killing in Pakistan of polio vaccination workers serves as the most recent example of health-related moral hazards that can arise in the pursuit of national and global security objectives. The deaths have been attributed to the Taliban, acting against health workers who have come under suspicion in the wake of the U.S.-led capture and killing of Osama bin Ladin. The capture of bin Ladin was made possible in part through the involvement of a doctor and other health workers, operating under the guise of a vaccination program. The killings and the distrust of health workers and programs are, thus, in part attributable to the counter-terrorism strategies deployed by military personnel working alongside security agencies. To take another example, the drones that fly over Waziristan and other Pakistani border areas have been shown to cause health consequences including anxiety and psychological trauma, physical injury, and death in civilian populations living below. The relationship between national security, foreign policy, and health has been explored in health diplomacy, aid and health, trade and health, infectious disease management, and health in conflict. However, research is needed on the ethical issues surrounding the global health impact of current counter-terrorism policy and practice. Given the ongoing nature of the ‘war on terror’, a dramatic escalation in the use of drones, and the demonstrated impact of these and other counter-terrorism strategies on the health of already vulnerable populations, on health and medical workers themselves, and on health and medical programs, a number of unexamined ethical issues and questions warrant urgent, careful attention. The workshop proposed here aims to assemble a diverse set of participants with essential expertise to identify and map the ethical issues surrounding the global health impact of current counter-terrorism policy and practice.