A complex Mus81-Mm4 is a DNA structure–specific endonuclease in Saccharomyces cerevisiae. Mus81-Mms4 functions in processing of recombination intermediates that could arise during the repair of stalled and blocked replication forks and double stranded breaks. Mus81-Mms4 works with many proteins involved in DNA repair, replication fork stability, and joint molecule formation/resolution during homologous recombination repair.