Chlorhexidine is used as a disinfectant to prevent surgical infections. Recently, studies have indicated that chlorhexidine usage has selected methicillin-resistant Staphylococcus aureus strains that are tolerant to chlorhexidine and that this may be related to the presence of the qacA/B-encoded efflux pumps. Here, we evaluated if high-level exposure to chlorhexidine selects for tolerant colonizing Staphylococcus epidermidis and we addressed the consequences of long-term exposure to chlorhexidine.