The Food and Agriculture Organization has established has established an international collaborative project for monitoring of avian influenza H5N1 virus variants in Indonesian poultry and defining an effective and sustainable vaccination strategy under the control of the OIE-FAO Network of Expertise for Animal Influenza (OFFLU). OFFLU guidance on vaccine strain selection states that all avian influenza vaccination programs should have epidemiologically relevant surveillance done to check for the emergence of genetic and antigenic variants. Since 2005 Indonesia has been the global hotspot for H5N1 infection in birds and humans. Due to the high level of H5N1 virus in poultry and the environment, and frequent contact between poultry and humans, Indonesia is widely regarded as having the highest risk of emergence of a new virus which may cause a human influenza pandemic. H5N1 has become endemic in poultry throughout much of Indonesia and vaccination can be a useful tool for short- to medium-term control if the vaccine is efficacious against the circulating field strains. Antigenic cartography was originally developed to characterize human H3N2 viruses and to facilitate selection of human vaccine candidate viruses by the WHO. This paper reports on the application of antigenic cartography to H5N1 viruses, the results of sequencing and antigenic analysis of Indonesian H5N1 virus isolates and the selection of relevant H5N1 vaccine candidates and challenge viruses for evaluating efficacy of new vaccines.