Avian influenza virus (AIV) monitoring in migratory birds has been performed in Taiwan since 1998. From 1998 to 2007, 29,287 samples were collected from wild ducks, shorebirds, and other wild birds in the four wetlands around Taiwan and at two outside islets, Penghu and Kinmen. Virus isolation was performed for all collected samples by inoculating chicken embryos. The AIV in the allantoic fluid was identified using hemagglutination and reverse transcription PCR. The AIV prevalence from those samples was 0.81% (237/29,287). The peak prevalence reached 1.06% (186/17,493) from September to December, during which time migrating ducks came from the North. The prevalence from January to April was 0.51%. However, no virus was isolated from May to August. The partial HA genes of 28 H4 AIVs were sequenced and analyzed. The phylogenetic tree showed that a correlation existed between the isolation years and the evolutional distances. The pathogenicity of the isolated H5 and H7 AIVs was determined by intravenous pathogenicity index (IVPI) testing in specific-pathogen-free chickens and by HA cleavage sequencing. Using the IVPI test and the HA cleavage sequences, all of the H5 or H7 AIVs isolated were determined to be low pathogenicity AIVs.