Efficient repair of double-strand breaks (DSBs) is important for the survival of all organisms. In principle, DSBs can be repaired via non-homologous end-joining (NHEJ) or via homologous recombination (HR). A major question of recent research was to elucidate under what condition which pathway is preferentially used (Paques and Haber, 1999). By expression of the rare cutting restriction endonuclease I-SceI we are analysing since a row of years the repair of DSBs in plants that harbour as a transgene a marker. In general, NHEJ seems to be the main mode of DNA repair in somatic plant cells (Kirik et al., 2000; Salomon and Puchta, 1998; for reviews see Gorbunova and Levy, 1999; Ray and Langer, 2002). However, homologous sequences can also be used for the repair of the break. We were able to show that information from allelic (Gisler et al., 2002) as well as ectopic sites (Puchta, 1999; see also Shalev and Levy, 1997 for a transposon-based approach) could be used for DSB repair at low frequencies. The fraction of HR in relation to NHEJ events increases if homologous sequences close to the break are available (intrachromosomal recombination) (Siebert and Puchta, 2002; see also Xiao and Peterson, 2000 for a transposon-based approach). However, because of the configuration of the applied recombination substrate, we were only able to monitor deletions between direct repeats in our previous study (Siebert and Puchta, 2002). Depending on the structure of the respective chromosomal locus, at least two different kinds of pathways may be used to repair the break. Whereas one pathway results (as described above) in the formation of a deletion between the repeats, the product of the other pathway is a gene-conversion event (Fishman-Lobell et al., 1992). The deletion pathway is explained best by a single-strand annealing (SSA) mechanism (Bilang et al., 1992; De Groot et al., 1992; Puchta and Hohn, 1991), whereas gene conversion can be explained by a synthesis-dependent strand-annealing (SDSA)-like-mechanism (Puchta, 1998; Rubin and Levy, 1997). Although several independent studies on DSB-induced intrachromosomal HR have been performed (Athma and Peterson, 1991; Chiurazzi et al., 1996; Siebert and Puchta, 2002; Xiao and Peterson, 2000; Xiao et al., 2000) because of differences in marker configurations, DSB induction, plant species, and detection assays, it was not possible to compare the results directly and to draw conclusions as to the efficiencies of the different pathways. Our recent results indicated that deletion formation is involved in up to one third of all repair events of a DSB when homologous sequences are close (Siebert and Puchta, 2002). The deletion-associated HR pathway can be efficiently induced by the excision of a transposon (Xiao and Peterson, 2000; Xiao et al., 2000). The occurrence of multiple single long terminal repeats (LTRs) of retroelements in cereal genomes (Vicient et al., 1999) indicates that this pathway might play an important role in plant genome evolution. Therefore, it was important to find out under comparable conditions to which extent the other pathway, being associated with gene conversion, can be used for the repair of DSBs by HR in somatic cells. In the current study, we now addressed this question using different repair constructs as transgenes. Our direct comparison indicates that the deletion-associated pathway is about five times more frequent than the pathway resulting in gene conversion. Nevertheless, gene conversion events can be drastically increased by DSBs and therefore may also contribute particularly to the evolution of tandemly arranged gene families, such as disease resistance genes.