Integrons have the capacity to capture small mobile elements known as gene cassettes, and this reaction is catalysed by integron-encoded Intl integrases. Intl integrases form a distinct family within the tyrosine recombinase superfamily and include a characteristic additional domain that is well conserved. Two different Intl enzymes were used to examine their ability to recognize heterologous attl sites in both integration and excision assays. Intl1 and Intl3 are 59% identical and catalyse both integrative and excisive recombination between a cassette-associated 59-be site and the cognate attl1 or attl3 site. Integrative recombination events involving a 59-be and a non-cognate attl site, attl2 and attl3 for Intl1 or attl1 and attl2 for Intl3, were detected extremely rarely. In cassette excision assays, the non-cognate attl3 site was recognized by Intl1, but attl1 was not well recognized by Intl3. The purified Intl1 and Intl3 proteins bound strongly only to their cognate attl site.