Suppression subtractive hybridisation (SSH) was performed to identify genomic differences between the uropathogenic Escherichia coli strain 536 and the non-pathogenic E. coli K-12 strain MG1655. In total, 22 DNA fragments were isolated which were specific for strain 536. Five of these fragments showed homology to known virulence determinants and four fragments matched genes for lipopolysaccharide (LPS) or capsule biosynthesis and a siderophore receptor. Seven fragments did not show any homology to known genes. These fragments may represent parts of putative pathogenicity islands (PAIs). Whereas two fragments were highly specific for uropathogenic E. coli (UPEC), the other fragments could also be detected among the other tested wild-type strains.