The Mre11-Rad50-Xrs2 complex in Saccharomyces cerevisiae has roles in the intra-S checkpoint, homologous recombination, non-homologous end joining, meiotic recombination, telomere maintenance and the suppression of gross chromosomal rearrangements (GCRs). The discovery of mutations in the genes encoding the human homologues of two MRX subunits that underlie the chromosome fragility syndromes, Ataxia telangiectasia-like disorder and Nijmegen breakage syndrome suggest that the MRX complex also functions in suppression of GCRs in human cells. Previously, we demonstrated that the deletion mutations in each of the MRX genes increased the rate of GCRs up to 1000-fold compared to wild-type rates. However, it has not been clear which molecular function of the MRX complex is important for suppression of GCRs. Here, we present evidence that at least three different activities of the MRX complex are important for suppression of GCRs. These include the nuclease activity of Mre11, an activity related to MRX complex formation and another activity that has a close link with the telomere maintenance function of the MRX complex. An activity related to MRX complex formation is especially important for the suppression of translocation type of GCRs. However, the non-homologous end joining function of MRX complex does not appear to participate in the suppression of GCRs.