Multidrug resistant Staphylococcus aureus are a major public major public health issue within our community. Understanding the molecular basis of S. aureus resistance mechanisms and how these genes are regulated is of critical importance if we are to turn the tide against the growing number of antimicrobial resistant bacteria. Within S. aureus, the qac efflux system confers resistance to a range of 30+ chemically and structurally diverse compounds, many of which are used as antiseptics and disinfectants. The qac system is composed of qacA and qacR which encode the QacA membrane-bound multidrug efflux pump and cytosolic QacR regulatory protein, respectively. The QacR protein transcriptionally represses qacA expression by binding to a region encompassing the qacA promoter in the absence of QacA substrates. QacR, unlike other members of the TetR family of repressor proteins, appears not to regulate its own expression via binding its own promoter. In this study we attempted to identify factors influencing qacR expression levels. Using a DNA protection assay, the DNA binding protein HU, a small regulatory protein commonly involved in cellular stress responses, was found to interact with the qacR regulatory region. Further examination of this relationship revealed that when the concentration of HU protein is increased, to mimic a stress response, qacR expression is repressed. These results indicate that the presence of a stress inducing antimicrobial compound could similarly lead to repression of qacR and consequently allow for optimum expression of qacA and expulsion of the compound. This work has thus shown for the first time a potential mechanism by which qacR is regulated. The elucidation of this regulatory mechanism therefore is the first step towards circumventing Qac-mediated multidrug resistance and reducing the risk of S. aureus infections.