U.S. service members are often deployed to regions endemic for malaria. Preventive measures play an important role in mitigating the risk of disease and adverse effects on mission performance. Currently, a large contingent of U.S. forces is deployed in malarious regions in southeast and southwest Asia. The purpose of this study was to describe malaria cases reported by the tri-service reportable medical events system in terms of exposure (deployment history) and latency of infection. We conducted a retrospective analysis of population health data routinely collected for disease surveillance. All malaria reports received into the Defense Medical Surveillance System by January 3, 2006 with a date of onset between January 1, 2000 and December 31, 2005 in which the individual diagnosed is a member of the active or reserve military components linked to personnel and deployment data were analyzed to determine assignment and deployment history. The main outcome measure was the ICD9-CM diagnosis of malaria (Plasmodium vivax, P. falciparum, P. ovale, P. malaria, and unspecified malaria) by date of onset and days from exposure. A total of 423 cases of malaria were reported during the study period. The Army (n = 325) and the Marine Corps (n = 46) had the highest number of reported cases. Plasmodium vivax (n = 242) and P. falciparum (n = 92) caused nearly four-fifths of all reported cases. During the period from 2003 through 2005, 34% of deployed cases were exposed to more than one malaria-endemic region. Seventy-four cases had been assigned in the Republic of Korea, and all were present in Korea during the high risk transmission period. Seventy-eight cases had documented service in Afghanistan; only 4 had off-season exposure and no other documented exposures. Sixty cases had documented exposure during Operation Iraqi Freedom (OIF). Only six seasonally exposed and six off seasonally exposed OIF cases had no other documented exposure. Fifty percent of Korean cases were diagnosed during an exposure season, and only 3% of Afghan cases were diagnosed during an exposure season. Soldiers in today's military can be exposed to more than one malaria-endemic region prior to diagnosis. This presents new complexities for disease monitoring and prevention policy development.