Methicillin-resistant Staphylococcus aureus (MRSA) strains are the major causative agents of numerous hospital-and community-acquired infections. Increasing prevalence of MRSA in cystic fibrosis (CF) populations is reported all over the world. Although there are papers reporting the prevalence and genetic backgrounds of MRSA isolates from different settings in Turkey, there is no information regarding the situation in the CF community. This study was conducted to characterize the MRSA strains recovered from CF patients followed-up at a Turkish reference CF centre. Microbiological testing of isolates was performed via conventional microbiological techniques. Molecular characterization of MRSA isolates was carried out by SCCmec typing by multiplex PCR and PVL gene determination. Among a total of 604 CF patients included in the study, 325 patients were found to harbour S. aureus (53.8%). Of those 325 patients, 24 were positive for MRSA during their follow-up (7.4%). Thirty-two MRSA isolates from these patients were chosen for further assessment of molecular characteristics. Twenty-six MRSA isolates exhibited a pattern like SCCmec type III (81.2%) and six consecutive MRSA isolates of a single patient revealed SCCmec type IV (18.7%). Our findings definitely support the need for further surveillance studies for CF-MRSA strains and highlight the need for infection control measures in the setting of CF centres.