The current concern of influenza is that avian influenza viruses transmit or provide to humans. Although the genomic information of human influenza A viruses is increasing, little of this type of data is available for viruses circulating in poultry farms. This study presented the genetic characterization of 9 H6N1 viruses isolated from chicken farms from 2000 to 2003. The whole complete eight genes of 3 avian isolates and the 6 genes of the rest 6 avian isolates were sequenced and compared. The phylogenetic trees of those genes demonstrate that influenza H6N1 viruses circulating in chickens in Taiwan are quite unique and different from those of other inbluenza viruses.