A unique aspect of meiosis is the segregation of homologous chromosomes at the meiosis I division. The pairing of homologous chromosomes is a critical aspect of meiotic prophase I that aids proper disjunction at anaphase I. We have used a site-specific recombination assay in Saccharomyces cerevisiae to examine allelic interaction levels during meiosis in a series of mutants defective in recombination, chromatin structure, or intracellular movement. Red1, a component of the chromosome axis, and Mnd1, a chromosome-binding protein that facilitates interhomolog interaction, are critical for achieving high levels of allelic interaction. Homologous recombination factors (Sae2, Rdh54, Rad54, Rad55, Rad51, Sgs1) aid in varying degrees in promoting allelic interactions, while the Srs2 helicase appears to play no appreciable role. Ris1 (a SWI2/ SNF2 related protein) and Dot1 (a histone methyltransferase) appear to play minor roles. Surprisingly, factors involved in microtubule-mediated intracellular movement (Tub3, Dhc1, and Mlp2) appear to play no appreciable role in homolog juxtaposition, unlike their counterparts in fission yeast. Taken together, these results support the notion that meiotic recombination plays a major role in the high levels of homolog interaction observed during budding yeast meiosis.M EIOSIS is the process by which a parent diploid cell undergoes one round of DNA replication followed by two rounds of chromosome segregation to yield haploid gametes. A unique aspect of meiosis is the segregation of homologous chromosomes at the first meiotic division. Nondisjunction, or improper segregation of homologs, at this stage can lead to gamete aneuploidy, which is a major cause of birth defects in humans (Hassold and Hunt 2001). Homologs are able to correctly orient toward opposite poles of the meiosis I spindle, because a collaboration of DNA crossovers (CR) with sister-chromatid cohesion forms temporary connections between the homologs (Page and Hawley 2003;Petronczki et al. 2003).Homologous chromosomes form progressively stronger associations as cells proceed through meiotic prophase I (Zickler and Kleckner 1999;Storlazzi et al. 2003). In the budding yeast, plants, and mammals, transacting factors required for meiotic recombination are crucial for the pairing and crossing over between homologous chromosomes. In contrast, synaptonemal complex (SC) formation, meiotic nuclear reorganization, and an achiasmate segregation system appear to play supplementary roles in meiotic homolog pairing in the budding yeast (Loidl et al.