India reported outbreaks of Highly Pathogenic Avian Influenza (HPAI) H5N1 in poultry in the states of Maharashtra, Gujarat and Madhya Pradesh (February–April 2006); Manipur (July 2007); West Bengal (January 2008) and Tripura (April 2008). The role of migratory birds in the transmission of the HPAI H5N1 remains a subject of debate. Avian Influenza (AI) surveillance in wild migratory, wild resident, domestic birds and poultry was undertaken by National Institute of Virology (NIV) jointly with Ela Foundation, Pune, India during 2006–07. A total of 1968 faecal specimens (1369 droppings from wild migratory and wild resident birds; 474 droppings from poultry and 125 cloacal swabs from chickens and ducks) were collected. These samples representing 10 avian families of wild migratory birds, four families of wild resident birds totalling 36 species, were from eight districts of Maharashtra covering 20 water bodies and two districts of Manipur. The samples were screened for AI viruses by reverse transcriptase polymerase chain reaction (RT-PCR), real-time PCR and were processed for virus isolation in embryonated chicken eggs and cell culture. Two samples from wild ducks were positive for viruses other than AI, newcastle disease virus (NDV) and infectious bursal disease virus (IBDV). During the study period no sample was positive for Influenza A viruses, Influenza A (H5N1) or any other strain of HPAI by RT-PCR and virus isolation. In view of the recent HPAI H5N1 outbreaks in poultry in India, continued and more widespread AI surveillance is necessary to elucidate the role of wild migratory, resident, domestic birds and poultry in the transmission of AI viruses.