Does military service, in particular operational deployment, result in a higher risk of chronic illness among military personnel and veterans? The Millennium Cohort Study, the largest Department of Defense prospective cohort study ever conducted, will attempt to answer this question. The probability-based sample of 140,000 military personnel will be surveyed every 3 years during a 21-year period. The first questionnaire, scheduled for release in summer 2001, will be sent to 30,000 veterans who have been deployed to southwest Asia, Bosnia, or Kosovo since August 1997 and 70,000 veterans who have not been deployed to these conflict areas. Twenty thousand new participants will be added to the group in each of the years 2004 and 2007 to complete the study population of 140,000. The participants will have the option of completing the study questionnaire either on the paper copy received in the mail or through the World Wide Web-based version, which is available at www.MillenniumCohort.org. This will be one of the first prospective studies ever to offer such an option. The initial survey instrument will collect data regarding demographic characteristics, self-reported medical conditions and symptoms, and health-related behaviors. Validated instruments will be incorporated to capture self-assessed physical and mental functional status (Short Form for Veterans), psychosocial assessment (Patient Health Questionnaire), and post-traumatic stress disorder (Patient Checklist-17). Information obtained from the survey responses will be linked with other military databases, including data on deployment, occupation, vaccinations, health care utilization, and disability. In addition to revealing changes in veterans' health status over time, the Millennium Cohort Study will serve as a data repository, providing a solid foundation upon which additional epidemiological studies may be constructed.