During meiotic prophase a number of important events require recombination between maternal and paternal chromosomes, which is initiated through the introduction of DNA double-strand breaks (DSBs). The majority of DSBs, which mostly occur at so-called hotspots, have been located between cohesin binding sites. qChIP (chromatin immunoprecipitation quantified by real-time PCR) is a sensitive, accurate, and cost-efficient alternative to ChIP-on-Chip for the analysis of noncovalent protein-DNA interactions at defined binding sites in vivo. Here we use qChIP to study Mre11 binding to three chromosomal loci during meiosis. We show that Mre11 interacts with a known hotspot region (UpsilonCR048) in the R-band of chromosome III, but not with a cold region in the G-band (UpsilonCR011). Interestingly Mre11 binds to a cohesin binding site (UpsilonCR067), 20 kb distal to UpsilonCR048, with similar intensity as to the hotspot, despite the absence of DSBs in this region.