Genes borne on cassettes are mobile owing to site-specific recombination systems called integrons, which have created various combinations of antibiotic resistance genes in R-plasmids. In these processes, the palindromic site, attC (59-base element), at cassette junctions has been proposed as being essential. Excised and circularized cassettes have been found to integrate with preference for an attl site at one end of the conserved sequence in integrons. In this work, we give evidence that recombination is possible in the absence of the highly organized attC sites between the more simply organized attl sites. Furthermore, at a very low frequency representing the background in our recombination assay, we observed cross-overs between attl and secondary sites. To characterize recombination excluding the attC sites, we have used naturally occurring attl variants and constructed mutants. The cross-over point was identified between a guanine and a thymine in attl using point mutations. Progressive deletions showed the extent of attl and identified two important regions in the conserved sequence 5' of the cross-over point. A region 27-36 bp 5' of attl influenced recombination with attC sites only, whereas a sequence 9-14 bp 5' of the cross-over point in attl was important for recombination with both attl and attC. Recombination between attl and secondary sites could allow fusion of the conserved sequence encoding the integron site-specific recombinase to new sequences.