The mobile element IS30 has dual target specificity, since it can integrate adjacent to the inverted repeat (IR) of another IS30 copy or into hot-spot sequences characterized by a well-defined consensus showing no similarity to the ends of the element. The result of such integrations into these targets is different, as gene conversion events take place frequently during insertion next to an IR end, while this phenomenon has never been observed in targeting hot-spot sequences. Conversion events in IR-targeting cannot be explained exclusively by the activity of the transposase, but suggest the involvement of the homologous recombination and repair machinery of the host cell. Here, we show that the homology between the donor and target sequences is required for conversion and the starting point of the process is the site of integration. The frequency of conversion depends on the distance of mutations from the end of the targeted element. Remarkable bias is found in the role of donor and target DNA, since generally the donor sequence is converted depending on the target. Conversion was shown to occur also without formation of transposition products. All these data are consistent with the idea of the establishment, migration and resolution of a Holliday-like cruciform structure, which can be responsible for conversion events. To explain the variety of conversion products in IR-targeting, a molecular model has been proposed and discussed.