In Asia, acute encephalitis is among the most frequent and severe causes of pediatric hospitalization. Moreover encephalitis etiologies remain unknown in more than 60% of patients. The surveillance and investigation of acute encephalitis syndrome is of utmost public health importance, both locally and globally. The workshop on infectious encephalitis in Southeast Asia held in Phnom Penh, Cambodia, from 12th to 15th February, 2012, was attended by around 40 participants representing French stakeholders from life and health sciences, and scientists from France and Southeast Asia. This new initiative is called the SEAe project, for SouthEast Asia encephalitis. It will bring together clinic-epidemiological data, state-of-the-art virology and wider perspectives from the social sciences. The implementation will first start with three selected pilot areas in Cambodia, Laos and Vietnam. The epidemiology unit at IPC will be responsible for auditing clinical sites in the three countries, training and implementing clinical data and samples collection and quality controls. Clusters of cases will trigger field investigations. The study should last three years.