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A molecular and serological study was carried out to determine the West Nile virus (WNV) status in different species of wild water birds. From 2003 to 2007, samples were collected from 519 birds representing 26 different species in Iran. Out of 519 serum samples tested for WNV antibodies, 78 (15%) were positive when tested using virus neutralization and immunofluorescence. Antibodies of WNV were detected in 71 out of 131 common coot (Fulica atra) samples. In comparison, only 7 out of 388 birds that were belonged to 25 other species of water birds revealed positive results. For most Anatidae species, no positive duck in serological tests was found. Further, no WNV viral RNA-positive samples were found in this study. Results of this investigation provide important information about the prevalence of WNV in wild water birds in Iran and indicate the potential role and importance of common coots in ecology of WNVs.