The Mre11 complex has been implicated in diverse aspects of the cellular response to DNA damage. We used in situ fractionation of human fibroblasts to carry out cytologic analysis of Mre11 complex proteins in the double-strand break (DSB) response. In situ fractionation removes most nucleoplasmic protein, permitting immunofluorescent localization of proteins that become more avidly bound to nuclear structures after induction of DNA damage. We found that a fraction of the Mre11 complex was bound to promyelocyte leukemia protein bodies in undamaged cells. Within 10 min after gamma irradiation, nuclear retention of the Mre11 complex in small granular foci was observed and persisted until 2 h postirradiation. In light of the previous demonstration that the Mre11 complex associated with ionizing radiation (IR)-induced DSBs, we infer that the protein retained under these conditions was associated with DNA damage. We also observed increased retention of Rad51 following IR treatment, although IR induced Rad51 foci were distinct from Mre11 foci. The ATM kinase, which phosphorylates Nbs1 during activation of the S-phase checkpoint, was not required for the Mre11 complex to associate with DNA damage. These data suggest that the functions of the Mre11 complex in the DSB response are implicitly dependent upon its ability to detect DNA damage.The human Mre11 complex, consisting of Mre11, Rad50, and Nbs1, functions in diverse aspects of the cellular response to DNA damage (43). Previous cytologic analyses have provided evidence that this complex associates with damaged DNA. This aspect of Mre11 complex function is diminished in human Mre11 complex mutants that exhibit S-phase checkpoint deficiency (44). We have therefore hypothesized that the complex influences the S-phase checkpoint either because it is itself a sensor of DNA damage or because it functions in close proximity to a sensor (8,48).In previous studies, we observed that the formation of ionizing radiation (IR)-induced foci (IRIF) of Mre11 complex proteins was strictly dependent upon the prior induction of double-strand breaks (DSBs). IRIF formation and IRIF multiplicity were influenced by the number of DSBs as well as by mutations affecting the DSB response. On that basis, the cytology of the Mre11 complex was inferred to reflect its role in the response to DSBs (35). Indeed, Mre11 complex IRIF formation has been used as an index of the DNA damage response in a variety of contexts (8,12,17,19,24,33,48,49,53,54).The interpretation that DSB-induced formation of Mre11 complex IRIF reflected an interaction with DNA damage was supported by the technique of partial-volume irradiation. This methodology permits the induction of DSBs in discrete subnuclear volumes and was used to demonstrate that the complex associates with DSBs while DSB repair is ongoing (39). In contrast, under the conditions previously employed, IRIF were detectable only at time points when the vast majority of DSB repair was complete. Thus, we have proposed that these structures represent Mre11 complex...