Homologous recombination can result in the transfer of genetic information from one DNA molecule to another (gene conversion). These events are often accompanied by a reciprocal exchange between the interacting molecules (termed "crossing over"). This association suggests that the two types of events could be mechanistically related. We have analyzed the repair, by homologous recombination, of a broken chromosome in yeast. We show that gene conversion can be uncoupled from crossing over when the length of homology of the interacting substrates is below a certain threshold. In addition, a minimal length of homology on each broken chromosomal arm is needed for crossing over. We also show that the coupling between gene conversion and crossing over is affected by the mismatch repair system; mutations in the MSH2 or MSH6 genes cause an increase in the crossing over observed for short alleles. Our results provide a mechanism to explain how chromosomal recombinational repair can take place without altering the stability of the genome.Homologous recombination is a universal process that plays a role in generating diversity during meiosis and is an important DNA repair mechanism in vegetative cells. Recombination results in the transfer of genetic information from one DNA molecule to a homologous one (gene conversion) and in the reciprocal exchange of DNA fragments between chromosomes (crossing over). The association between gene conversion and crossing-over events has led to the assumption that they are mechanistically related (Refs. 1-5; Fig. 1). One of the characteristic features of most eukaryotic genomes is the presence of large amounts of repetitive DNA. Reciprocal recombination between dispersed repeats may result in chromosomal aberrations, such as deletions, translocations, etc., that can affect the reproductive fitness of an organism or lead to cancer. Therefore, to maintain the genome integrity, crossing over must be prevented during recombinational repair of DNA lesions involving dispersed repeats. Double-strand breaks (DSBs) 1 in the DNA of living organisms occur as a consequence of the natural cell metabolism, or they can be created by exogenous sources such as chemical agents or radiation. If left unrepaired, DSBs result in broken chromosomes and cell death (6). Mitotic recombination plays an important role in the repair of this damage. In addition, DSBs are generated during certain developmental processes such as meiosis (7) and mating-type switch in yeast (8). In different experimental systems, it was found that the level of association between gene conversion and crossing over varies, from no coupling (e.g. mating-type switch (8 -10) or recombination between direct repeats (11)) to a level of association of 70% (5). In two of the currently held models of recombination, the synthesisdependent strand annealing (SDSA) model (12) and the DSB repair model (4), recombination is initiated by the creation of a DSB in one of the two participating DNA duplexes (Fig. 1). Although the mechanism suggested by the SDS...