Introduction: The Mortality Surveillance Division (MSD) of the U.S. Armed Forces Medical Examiner System was established in 1998 to improve surveillance for all military deaths although emphasizing deaths from infectious diseases. Establishment of the MSD was part of the 1997 Department of Defense initiative to improve surveillance and response for emerging infectious diseases. Before 1998, mortality surveillance was limited to compiling information from death certificates, a system that provided limited useful information and lacked the timeliness needed to take meaningful action to address emerging infectious disease threats. Materials and Methods: The MSD was tasked to quickly identify all infectious disease deaths and the infecting agents. The system developed by the MSD staff identified deaths in near real-time and immediately notified military Public Health authorities of situations that warranted an investigation. Autopsy, medical, and investigative reports were collected. Testing specimens for agent identification was encouraged. The data and information collected were archived in the MSD-developed Medical Mortality Registry (MMR), a database that included all active duty Service Member deaths and contained manner and cause of death with medical, demographic, circumstantial, and diagnostic information. The MMR was the only comprehensive, autopsy-based source for mortality information on active duty military deaths. Results: During 1998–2013, 217 (1.3%) infectious disease deaths were identified among 16,192 noncombat deaths. Of the 217 deaths, 29.5% were classified as respiratory, 18.0% cardiac, 15.2% blood borne, 12.9% nervous system, and 12.4% sepsis. A pathogen was identified for 64.5%. Agents of military interest identified included Neisseria meningitidis, influenza viruses, adenoviruses, and malaria. Neisseria meningitidis was identified in 10 fatal cases; grouping of the agent was done for eight cases. Four were group B, two were C, and two were Y. All eight had been immunized with a quadrivalent meningococcal vaccine. The most commonly detected respiratory agent was influenza virus (nine deaths), three of which were the 2009 pandemic H1N1 influenza virus. Adenoviruses were identified as the infectious agents in a total of nine deaths. Two deaths resulted from Plasmodium falciparum malaria infections acquired in Africa during military deployments. An important but unexplained finding was that Black Service Members made up only16.3% of all military personnel but accounted for 28.6% of all infectious disease deaths. Conclusion: The time lag between death and notification of the MSD at the start of this surveillance program was 24 to 48 hours. The lag at the end of the reported surveillance period was 8 to 24 hours. The MSD surveillance system identified an agent in 140 of 217 (64.5%) uniformed deaths. In a similar program by the Centers for Disease Control and Prevention, in 122 cases with specimens, an agent could be identified in 34 (28%). MMR data and information provided strong support for re-establishing the military recruit adenovirus vaccination program, which ceased in 1999 and was finally re-established in 2011. MMR data and information also assisted in monitoring the military meningococcal vaccine program, helped to describe the virulence of circulating influenza viruses, and identified areas where deadly malaria infections were not being prevented.