Emerging and zoonotic infectious diseases are a major issue in Indonesia. The objective of this mission, funded by the Institut Français d'Indonésie (IFI), was to identify potential subjects of collaboration between CIRAD, Pasteur Institute, and Indonesian universities, research centers, and organizations. Meetings were held in Jakarta, Bogor and Yogyakarta with representatives of FKUI, the Ministry of Health, the Ministry of Agriculture, the DICs of Denpasar and Kupang, CIVAS, ICASEPS, LIPI, IPB, UGM, UNUD, and FAO. The mission went very well and had very positive outcomes: we were warmly welcomed by our colleagues, had fruitful discussions and identified promising grounds for future collaborations on zoonoses and emerging diseases. The first field of collaboration could be training. Training modules and exchange of staff and students could be organized quite easily and rapidly, especially through the GREASE regional network for the management of emerging epidemiological risks in Southeast Asia or the Institut Pasteur International Network. Some funds should be available at IFI to initiate such training and exchanges. Two fields of research were identified for a second stage of collaboration: rabies and wildlife health. Regarding rabies, comparative and integrated approaches could be used to address research gaps on dog ecology, inter?islands movements of dogs, knowledge attitude and perception regarding dog ownership and rabies, spatial and temporal dynamics of rabies, and exploration of potential wildlife reservoirs. Ideally, these studies would be conducted in islands with different epidemiological contexts. Flores would be a good candidate to start with as this island has benefited from limited rabies research despite the fact that it has experienced more than 200 human rabies cases since the disease first occurred in 1997. Regarding wildlife health, most of the work conducted thus far pertained to conservation medicine for endangered species. There is a strong