The Military Health System (MHS) of the US Department of Defense (DoD) provides comprehensive medical care to over nine million beneficiaries, including active-duty members, reservists, activated National Guard, military retirees, and their family members. The MHS generates an extensive database containing administrative claims and medical encounter data, while the DoD also maintains a cancer registry that collects information about the occurrence of cancer among its beneficiaries who receive care at military treatment facilities. Collating data from the two sources diminishes the limitations of using registry or medical claims data alone for cancer research and extends their usage. To facilitate cancer research using the unique military health resources, a computer interface linking the two databases has been developed, called Military Cancer Epidemiology, or MilCanEpi. The intent of this article is to provide an overview of the MilCanEpi data system, describing its components, structure, potential uses, and limitations.