Background and Aims: Influenza A virus infects birds and some mammalian including human. H1 and H3 subtypes are circulated in both human and birds' population. To determine the prevalence of the mentioned subtypes in birds, different captive bird species in Tehran zoo, and affiliated centers in Tehran were investigated for virus infection. Methods: In this study, Between November 2008 and February 2009, 76 cloacal swabs and serum samples were collected from 5 orders of Anseriformes, Galliformes, Columbiformes, Pelicaniformes and Phoenicopteriformes. Antibody surveillance was undertaken by haemagglutination inhibition assay and for detection of influenza virus genome RT-PCR technique was used. Results: In total, 57.7% and 88.75% of bird sera were seropositive against H1 and H3 viruses respectively. The highest GMT value and the greatest antibody titers were observed in Galliformes order particularly in chicken species. Influenza A genome was not detected in any of the samples by RT-PCR using M gene. Conclusion: Results of this study indicated that seropositive birds were infected during the last or possibly previous years with H1 and H3 virus strain.