Reported cases of malaria in the Navy and Marine Corps were reviewed from the Naval Disease Reporting System (NDRS) and the Defense Medical Epidemiological Database (DMED). For 1997 through 2000, NDRS identified 62 cases of malaria and DMED identified 162 cases. Further analysis compared NDRS and DMED information with Composite Health Care System (CHCS) records in the Hampton Roads catchment area. The review of 46 patient records available in CHCS found that 30 patient encounters were miscoded in DMED for malaria treatment when they were actually for malaria chemoprophylaxis, 12 visits were coded for malaria treatment, and 4 visits had no apparent relationship to malaria. Ten of the 12 patients reported as treated for malaria in CHCS were also recorded in NDRS. This review suggests a need for further analysis and additional efforts to improve reporting and coding compliance to enhance medical surveillance and force health protection.