The Australian Government has supported the establishment of a Deployment Health Surveillance Program for the Australian Defence Force. Although some health screening mechanisms already exist for Australian Defence Force personnel, until now health data have been used largely for clinical management at an individual level and have not been aggregated to identify trends in health and risk factors in the shorter or longer term. We identify challenges for and potential benefits of health surveillance in the military context, describe features of the Program and progress to date. Retrospective and cross-sectional projects based on deployments to the Near North Area of Influence since 1997 are under way. A planned prospective model of health surveillance for those deploying to the Middle East promises more timely attention to any emerging health problems for military personnel and veterans.