Background. Autochthonous malaria does not currently occur in Jakarta, the most populous city in Indonesia. Military, forestry, mining, and tourist activities draw Jakarta residents to distant parts of the archipelago with high rates of malaria. Although malaria is a reportable disease in Jakarta, little has been published. Methods. We collected demographic and travel information from patients in Jakarta with microscopically confirmed malaria from January 2004 to February 2005, using a standardized data collection form. These results were compared to regional rainfall statistics and transit patterns of Jakarta residents to and from rural areas. Results. Data from 240 patients were collected. Aceh Province was the travel destination most commonly recorded for military members, while Papua and Bangka Island were the most frequently cited by civilians. Plasmodium falciparum accounted for 53% of cases, of which 15% had detectable gametocytemia. The most common admission diagnoses were malaria (39%), febrile illness not otherwise specified (23%), viral hepatitis (19%), and dengue (11%). The median time from admission to microscopic diagnosis was 2 days for civilian patients and 2.5 days for military patients. The highest number of cases occurred in May, July, and December with the nadir in October. Conclusions. The diagnosis of malaria may be overlooked and therefore delayed, in nonendemic areas such as Jakarta. Travel destinations associated with contracting malaria vary significantly for civilian and military populations. The factors affecting the peak months of importation likely include rainfall, holiday transit, military flight availability, and referral center locations.