Despite the fact that eukaryotic cells enlist checkpoints to block cell cycle progression when their DNA is damaged, cells still undergo frequent genetic rearrangements, both spontaneously and in response to genotoxic agents. We and others have previously characterized a phenomenon (adaptation) in which yeast cells that are arrested at a DNA damage checkpoint eventually override this arrest and reenter the cell cycle, despite the fact that they have not repaired the DNA damage that elicited the arrest. Here, we use mutants that are defective in checkpoint adaptation to show that adaptation is important for achieving the highest possible viability after exposure to DNA-damaging agents, but it also acts as an entrée into some forms of genomic instability. Specifically, the spontaneous and X-ray-induced frequencies of chromosome loss, translocations, and a repair process called break-induced replication occur at significantly reduced rates in adaptation-defective mutants. This indicates that these events occur after a cell has first arrested at the checkpoint and then adapted to that arrest. Because malignant progression frequently involves loss of genes that function in DNA repair, adaptation may promote tumorigenesis by allowing genomic instability to occur in the absence of repair.Cell cycle checkpoints are thought to provide time for DNA repair by delaying cell cycle progress in the face of DNA damage (reviewed in reference 21). Saccharomyces cerevisiae arrests in metaphase for up to 8 h when chromosomes are damaged (e.g., by a double-stranded DNA [dsDNA] break), after which it adapts and continues through the cell cycle (12,18,20). Two classes of proteins have been identified that are required for checkpoint adaptation: repair proteins and signaling proteins. Mutations in KU increase the amount of singlestranded DNA that forms at a dsDNA break, thereby increasing the strength of the checkpoint signal and eliminating adaptation (13). Strains in which the casein kinase II specificity subunits (CKB1 or CKB2) are deleted or that contain a special allele of the gene encoding the polo kinase Cdc5p (cdc5-ad) are also unable to adapt to DNA damage arrest (20).dsDNA breaks can be processed by many mechanisms that result in different outcomes. Archetypal homologous recombination (reattachment of two broken ends using a homologous template) allows error-free repair. However, other, more error-prone outcomes are also seen: (i) nonhomologous end joining results in deletions; (ii) single-strand annealing (SSA) between direct repeats results in deletions; (iii) break-induced replication (BIR) can yield translocations or large gene conversion tracts that cause loss of heterozygosity; (iv) ectopic telomere addition causes terminal truncations; and (v) unrepaired chromosomes may be lost altogether (reviewed in references 4 and 5). Each of these pathways can lead to the loss of genetic information (genomic instability). Which of these scenarios occurs may depend upon where the cell is in the cell cycle when it repairs the damage...