Pathways of DSB repair need to be able to repair a wide variety of damage products. Part of this flexibility is achieved by the recruitment of various repair factors as required, meaning that the NHEJ pathway can have a range of outcomes depending on the repair components involved. This is also illustrated by the activities of alternative NHEJ pathways for DSB repair that operate in the absence of one or more of the conserved NHEJ components, and there is much debate in the literature as to what extent these represent distinct pathways or a range of factors that can contribute through recruitment to a central mechanism (Lieber, 2010; Mladenov & Iliakis, 2011). In mammals, backup NHEJ pathways (B-NHEJ) independent of KU have been described, including microhomology-mediated end joining (MMEJ) and alternative NHEJ (alt-NHEJ or A-NHEJ). In some cases these display greater dependence on microhomologies, and identified B-NHEJ factors include the MRN complex, PARP and the XRCC1–DNA ligase 3 complex (Mladenov & Iliakis, 2011) Evidence for KU- and LIG4-independent DSB repair is also well established in plants (reviewed in Bray & West, 2005). Recently, a number of studies have identified components of these alterative end-joining pathways in plant cells and the corresponding mutant lines display slowed rates of DSB repair. Analysis of repair kinetics enables distinct phases of DSB repair corresponding to different repair pathways to be distinguished in plants. Repair kinetics have been analysed using two independent methods to quantify DNA damage: single cell electrophoresis (the comet assay) employs electrophoretic analysis of individual nuclei and image analysis to quantify levels of fragmented DNA, while immunocytochemistry detects the formation and disappearance of DNA damage foci using antisera to phosphorylated histone γH2AX. Currently technical limitations in plants mean that γH2AX detection can only be performed in M-phase cells, so caution is required in direct comparisons between repair kinetics measured by γH2AX foci and data obtained using the comet assay, which averages results from a mixed population of cells derived from whole seedlings. DSB repair in Arabidopsis displays an initial rapid phase of repair followed by a slower phase(s) of repair with half the breaks repaired within c. 6 min, as determined by the comet assay (Kozak et al., 2009), and c. 40 min, as assayed by analysis of H2AX foci (Charbonnel et al., 2010). Detailed analysis of repair kinetics in mutant lines has implicated a number of proteins in alternative DSB repair pathways in higher plants, including those also associated with plant SSB repair pathways (DNA LIGASE 1 (LIG1) and XRCC1) (Waterworth et al., 2009; Charbonnel et al., 2010). These studies also identified roles for the structural maintenance of chromosomes-like proteins MIM and RAD21.1, which may function to stabilize the DSB and are required for the initial rapid phase of repair (Kozak et al., 2009). It has also been shown that KU80 and XRCC1 act redundantly in the initial stages of repair (Charbonnel et al., 2010). Further analysis of the backup pathways in Arabidopsis investigated repair activities in plants mutated in the known DSB repair factors: KU80, XRCC2 (homologous recombination), XRCC1 (DSB repair using single-strand break repair proteins) and XPF (single-strand break repair and single-strand annealing of double-strand breaks, including MMEJ), both singly and in combination. The conclusions from this study were that there is a hierarchy of DSB repair pathways, with KU-dependent end joining being the major pathway in plants, but that in the quadruple ku80 xrcc1 xrcc2 xfp mutants an uncharacterized DSB repair pathway was active even in the absence of all four repair factors (Charbonnel et al., 2011). These studies clearly reflect the very robust mechanisms for DSB repair present in plant cells.