To identify unique DNA fragments associated with avian pathogenic Escherichia coli strains, suppression subtractive hybridization (SSH) was used. The genome of nonpathogenic E. coli K-12 strain MG1655 was subtracted from the genome of avian highly pathogenic strain E037 (serotype O78) resulting in the identification of 17 specific fragments. And the genome of avian low pathogenic E. coli strain E526 (serotype O2) was subtracted from the genome of avian highly pathogenic strain E058 (serotype O2) resulting in the identification of 32 specific fragments. Sequence homology analysis was done and four types of fragments were identified: plasmid sequences, phage sequences, sequences with known function and sequences without any currently known function. And 12 specific fragments that were not found in E. coli K-12 were identified from two avian E. coli strains. The results suggested that there were some genetic differences between the highly pathogenic strains and low pathogenic or nonpathogenic strains.