A monitoring programme has been initiated in Bavaria to continuously control wild birds for the presence of avian Influenza A virus (AIV) and to monitor the possible occurrence and accumulation of notifiable AIV subtypes as an early-warning system. In addition information about the regional, seasonal and species-specific distribution of AIV could be obtained. Between July 2007 and December 2008 samples from 5864 wild birds of twelve different zoological orders had been collected (cloacal- and tracheal swab samples, droppings, and organs) and analysed. AIV genomes were detected in 3.7% of the 5864 wild birds by RT real time PCR. The subtype component H5 was identified in 52 samples (0.9%) and the N1 subtype component in 13 samples (0.2%), but never in combination with each other. The hemagglutinine subtype component H7 could not be detected. Most of the positive AIV genome results originated from samples in the district Swabia, which is situated in the central area of the south-west bird migration route across southern Germany and harbours favourable resting areas for migrating birds. Mallards (Anas platyrhynchos) were the most frequently sampled bird species and had the highest AIV infection rate of 6.4%, followed by Tufted ducks (Aythya fuligula) (AIV prevalence of 5.4%), Mute Swans (Cygnus olor) (1.6%), Coots (Fulica atra) (0.3%) and Greylag Goose (Anser anser) (0.1%). The detection rate of AIV in Bavarian wild birds showed a seasonal peak in autumn/winter. Ten virus isolates could be obtained after sample inoculation in embryonated hen's eggs.