In Java, Indonesia, during March 2007-March 2008, 96 farms with scavenging ducks that were not vaccinated against highly pathogenic avian influenza (HPAI) were monitored bimonthly. Bird-level (prevalence among individual birds) H5 seroprevalence was 2.6% for ducks and 0.5% for chickens in contact with ducks. At least 1 seropositive bird was detected during 19.5% and 2.0% of duck- and chicken-flock visits, respectively. Duck flocks were 12.4x more likely than chicken flocks to have seropositive birds. During 21.4% of farm visits, <or=1 sampled duck was H5 seropositive when all sampled in-contact chickens were seronegative. Subtype H5 virus was detected during 2.5% of duck-flock visits and 1.5% of chicken-flock visits. When deaths from HPAI infection occurred, H5 virus shedding occurred in apparently healthy birds on 68.8% of farms. Of 180 poultry deaths investigated, 43.9% were attributed to H5 virus. These longitudinal study results indicate that ducks are a source of infection for chickens and, potentially, for humans.