The United States Naval Medical Research Unit 2 (NAMRU-2), has been located in the Republic of Indonesia since 1970. The host of NAMRU-2 is the Indonesian Ministry of Health, National Institute of Health Research and Development. The collaboration of Indonesian and U.S. Navy medical entomologists over the last 36 years has lead to ground breaking research on Filariasis, Dengue, Malaria, Plague, Chickungunya, Japanese Encephalitis, Scrub typhus and their associated insect vectors in Indonesia. Current projects include determining malaria vector distribution using fieldwork, Remote Sensing and GIS, Aedes aegypti and Dengue surveillance in Jakarta, Bionomics of malaria vectors in West Java, GIS and malaria control in Banda Aceh, and development of an exposure-free bednet trap for insect vectors. Current and past medical entomology research conducted at NAMRU-2 will be discussed in the context of its importance to the control of vector borne diseases in Indonesia.