To define avian influenza virus prevalence in wild birds in Bavaria, 12 930 tracheal, cloacal swabs or tissue samples from various waterfowl species were screened between January 2006 and December 2007. In 291 (2.3%) birds, genomes of influenza A viruses were detected by reverse transcription real-time PCR (rRT-PCR) targeting the matrix protein genes. Furthermore, solitary H5 hemagglutinin or N1 neuraminidase encoding genes were identified in 35 (0.3%) apparently healthy birds; whereas highly pathogenic (HPAI) H5N1 virus genomes were only diagnosed in dead wild birds (n = 93; 0.7%) found across this federal state region. In this study, multiple import events for H5N1 viruses were confirmed during 2006 and 2007. In addition, our findings argue against an existing HPAI H5N1 reservoir in aquatic birds in Bavaria. By contrast, phylogenetic analyses of the H5 or N1 sequences of low pathogenic avian influenza (LPAI) viruses revealed a marked diversity and multiple genetic lineages. This diversity of LPAI H5 and N1 subtype components indicates the existence of LPAI HA and NA gene pools which differ from the Bavarian HPAI H5N1. Moreover, the hemagglutinin amino acid differences between LPAI H5 viruses of a western European genotypic lineage observed in wild birds suggest a continuous evolution of LPAI viruses in Bavaria.