Objective To investigate the disinfectant-resistant gene qacA in Staphylococcus aureus isolates from the First Affiliated Hhospital of Chongqing Medical University. Methods A total of 126 S. aureus strains were isolated. The minimum inhibitory concentrations (MICs) of 4 representative monovalent and bivalent disinfectants were determined. Polymerase chain reaction (PCR) was employed to analyze the prevalence of qacA gene in these strains. Disk diffusion method was used to identify methicillin-resistant S. aureus (MRSA).Results Of the 126 S. aureus strains, 12 were positive for qacA gene. The prevalence of qacA in these strains was 9.5%. The prevalence of qacA gene in MRSA was 17.3%. Conclusions qacA gene is prevalent in the clinical isolates of S. aureus.