Wild waterbirds sampled July 2006–September 2009 in Mongolia were tested for antibodies to avian influenza (AI) virus with the use of a commercially available blocking enzyme-linked immunosorbent assay. Antibodies were detected in 25% (572/2,282) of tested birds representing 26 species, and all antibody-positive samples were from 12 species in the orders Anseriformes and Charadriiformes. The highest antibody prevalence was in Ruddy Shelducks (Tadorna ferruginea; 61.7%; n=261; 95% confidence interval [CI] 55.8–67.6%), Whooper Swans (Cygnus cygnus; 38.4%; n=242; 95% CI 32.3–44.5%), Swan Geese (Anser cygnoides; 15%; n=127; 95% CI 8.6–21.4%), Bar-headed Geese (Anser indicus; 13%; n=738; 95% CI 10.3–15.1%), and Mongolian Gulls (Larus mongolicus; 3.9%; n=255; 95% CI 1.3–6.5%). There was no significant temporal or spatial variation in the presence of antibodies in the sampled species. However, Bar-headed Geese and Mongolian Gulls showed spatial variation in antibody prevalence in 2007 and 2008, respectively. Our study provides insights into the hatch year waterbirds' exposure to AI virus at their natal and molting sites in Mongolia.