The Institute of Tropical Medicine, of Nagasaki University (ITM) and the National Institute of Hygiene and Epidemiology, Vietnam (NIHE), have been jointly conducting a joint project since 2005 on emerging and reemerging infectious diseases under a grant from the Ministry of Education, Science, Culture and Technology (MEXT) of Japan. A Vietnam research station established on the NIHE campus has been the site of a number of research activities. Project for clarifying environmental and social factors affecting outbreaks of zoonosis, vector-borne infectious diseases, diarrhoea, and childhood pneumonia have been conducted within a collaborative project framework. Having achieved the goals set or research in the project's first phase (from 2005 to 2009), the next objectives have been underlined, clarifying the factors and mechanisms causing infectious diseases. Four groups were established to answer these research questions, i.e., diarrhoea, vector-borne disease, clinical epidemiology, and zoonosis. These groups have conducted 15 independent activities. To conduct projects on a higher level, cooperation has been established with three Vietnamese governmental research institutions and with JICA-supported national hospitals. The outcome of such activities is expected to contribute greatly to promoting public health and improving medical care.