A site-specific recombination system that probes the relative probabilities that pairs of chromosomal loci collide with one another in living cells of budding yeast was used to explore the relative contributions of pairing, recombination, synaptonemal complex formation, and telomere clustering to the close juxtaposition of homologous chromosome pairs during meiosis. The level of Cre-mediated recombination between a pair of loxP sites located at an allelic position on homologous chromosomes was 13-fold greater than that between a pair of loxP sites located at ectopic positions on nonhomologous chromosomes. Mutations affecting meiotic recombination initiation and the processing of DNA double-strand breaks (DSBs) into single-end invasions (SEIs) reduced the levels of allelic Cre-mediated recombination levels by three-to sixfold. The severity of Cre/loxP phenotypes is presented in contrast to relatively weak DSB-independent pairing defects as assayed using fluorescence in situ hybridization for these mutants. Mutations affecting synaptonemal complex (SC) formation or crossover control gave wild-type levels of allelic Cre-mediated recombination. A delay in attaining maximum levels of allelic Cre-mediated recombination was observed for a mutant defective in telomere clustering. None of the mutants affected ectopic levels of recombination. These data suggest that stable, close homolog juxtaposition in yeast is distinct from pre-DSB pairing interactions, requires both DSB and SEI formation, but does not depend on crossovers or SC.[Key Words: Meiosis; homolog pairing; recombination; synaptonemal complex; budding yeast] Received February 11, 2002; revised version accepted May 8, 2002. During meiosis, chromosomes are segregated sequentially in two different ways. In the first meiotic division, homologous chromosomes segregate from one another. In the second meiotic division, as in mitosis, sister chromatids segregate from one another. Interactions between homologous chromosomes develop and are stabilized throughout meiosis I prophase at both the DNA level and at the homolog-axis level. Events contributing to these interactions include pairing, recombination, synapsis, and telomere clustering (for review, see