Respiratory infection is very common in patients suffering from cystic fibrosis (CF). However, the antimicrobial resistance rate of isolates from CF patients is not often documented. In this study, 279 respiratory specimens of 146 “patients” were prospectively collected from July to December 2006. Microbiological cultures and antimicrobial susceptibility tests of the most frequently isolated bacteria were performed. Sputum and oropharyngeal swabs were processed for culture. During the study period, 50% of the patients harbored Staphylococcus aureus, 35% Pseudomonas aeruginosa, 4.7% Haemophilus influenzae. Methicillin resistant S. aureus (MRSA) were detected in 8 (6%) patients; ESBL and MBL-producing P. aeruginosa were not identified in these patients. The detection of MRSA in CF patients confirms that antimicrobial resistance patterns should be always kept under surveillance. Moreover, hygiene regulations in CF clinics should prevent a further spread of resistant bacterial strains.