In uropathogenic Escherichia coli strain 536, six pathogenicity islands (PAIs) encode key virulence factors. All PAIs except PAI IV536 are flanked by direct repeats and four of them encode integrases responsible for their chromosomal excision. To study recombination sites used for the integration by PAI II536 and III536 integrases, we measured site-specific recombination between the chromosomal integration site attB, and the PAI-specific attachment site attP. We show that PAI III536 IntB, but not IntA, mediates PAI III536 integration. Studies of integrative recombination sites of both PAIs show that, when using a large cognate attP site (839 bp for PAI II536 and 268 bp for PAI III536), PAI II536 and III536 attB sites could be reduced to 16 bp and 20 bp, respectively, without affecting recombination. Further reduction to 14 bp for PAI II536 and 13 bp for PAI III536 diminished recombination efficiency. Surprisingly, attP sites could also be reduced to 14 bp (PAI II536) and 20 bp (PAI III536). The integration host factor (IHF) and the DNA-bending HU protein do not influence PAI II536 recombination, but IHF enhances PAI-III536 excision and negatively affects its integration. These data suggest that PAI intasomes differ from those of lambda and P4 integrase paradigms.