Development of resistance to disinfectant substances in nosocomial microorganisms is an important problem encountered during disinfectant practices. Methicillin-resistant Staphylococcus aureus (MRSA) remains a significant cause of hospital-acquired infections. Besides being resistant to several antimicrobial agents, MRSA strains can also become resistant to some disinfectant substances. Resistance to disinfectant substances may develop due to the misuse of disinfectants. This may either be due to the frequent use of disinfectant substances or use in lower concentrations than recommended. MRSA strains may harbour the qacA/B disinfectant resistance genes that may cause resistance to quarternary ammonium compounds and some cationic disinfectants. These resistance genes are found in plasmids and are responsible for decreased susceptibility or resistance. In this study, a total of 69 nosocomial MRSA strains isolated from clinical specimens in our hospital were tested for disinfectant activity and the presence of qacA/B disinfectant resistance genes in these isolates was investigated by polymerase chain reaction. We determined whether the presence of these genes caused phenotypic resistance to chlorhexidine and benzalkonium chloride by the use of bactericidal and bacteriostatic tests. For this purpose, the minimum inhibitory concentration (MIC) values of these disinfectants against MRSA isolates were detected by microdilution method with the proposals of CLSI, and bactericidal effects of these disinfectants were also detected by using quantitative suspension test according to EN13727:2003 European Standard. It has been found that 11.6% (8/69) of the isolates harbored qacA/B resistance genes. MIC values for chlorhexidine and benzalkonium chloride were found in the range of 2-8 mu g/ml. Although it was observed that MIC values were higher in five of the qacA/B gene positive isolates, statistically significant difference was not found between gene positive and gene negative groups. Both 1% chlorhexidine and 1% benzalkonium chloride were found bactericidal against the isolates including the ones carrying the qacA/B resistance genes. It was concluded that the presence of the qacA/B disinfectant resistance genes did not lead to resistance to the disinfectant substances at the concentrations used in clinical practices. Furthermore, tested disinfectants still exhibited bactericidal activity even with high MIC values.