Although bacteria lack the proteasome-ubiquitin proteolytic pathway, the homologue of the beta-type proteasome subunit, ClpQ, is highly conserved among bacterial species. ClpQ associates with its ATPase partner, ClpY, to form a two-component protease, which also structurally resembles the 26S proteasome. Here we have disrupted clpQ and clpY of the versatile pathogen Staphylococcus aureus in order to examine the significance of the ClpYQ protease for growth under stress conditions. We found that the mutant, in contrast to the wild type, was unable to form colonies at very high temperatures. To our knowledge, this is the first-described phenotype of ClpYQ in Gram-positive bacteria. However, in the presence of puromycin and under all other stress conditions, tested growth of the clpYQ mutant cells was similar to growth of the wild type. Additionally, the absence of ClpYQ did not affect virulence as measured by a murine skin abscess model. Transcriptional analysis revealed that clpQ and clpY are expressed as part of a four-cistronic operon encompassing xerC and codY, and that expression is modestly induced by heat. In conclusion, our data indicates that ClpYQ plays only a secondary role in the degradation of non-native proteins in S. aureus.