In response to concerns about the health effects of deployments following the 1991 Gulf War, the Congress and the Institute of Medicine recommended that DoD conduct prospective epidemiological research to evaluate the impact of military exposures, including deployment, on long-term health outcomes. The Millennium Cohort Study, the largest prospective health study in the military with more than 200,000 participants, meets this critical need. Although the original designers of the Millennium Cohort Study could not foresee the post-2001 military conflicts, the project is perfectly positioned to address health outcomes related to these operations. As force health protection continues to be a priority for the future of the United States military, the Millennium Cohort Study will be providing critical information towards enhancing the long-term health of future generations of military members.