Staphylococcus aureus is one of the first pathogens which often persistently infect the airways of cystic fibrosis (CF) patients. Nasal S. aureus carriage is a risk factor for S. aureus infections in non-CF patients. Topical treatment strategies successfully eradicate nasal S. aureus carriage, thereby decreasing S. aureus infection. A prospective longitudinal multicenter study was conducted to assess whether nasal carriage represents a risk factor for S. aureus colonization of the oropharynx in young CF patients. Cross-sectional analysis revealed a significantly higher prevalence of S. aureus-positive nasal (28/80 [35%] versus 20/109 [18%]; P < 0.01) and oropharyngeal (35/80 [44%] versus 20/109 [18%]; P < 0.001) cultures in children with CF compared to a control group. The first site of S. aureus detection was the nose in 6 patients and the oropharynx in 14 patients, respectively. Longitudinal analysis demonstrated a significantly higher S. aureus prevalence (61/62 [98%] versus 47/62 [76%]; P < 0.001) and persistence (46/62 [74%] versus 31/62 [50%]; P < 0.01) in the oropharynx than in the nose. In CF patients, the oropharynx, and not the nose, was the predominant site of S. aureus infection and persistence. Hence, it is unlikely that CF patients will benefit from topical treatment strategies to eradicate nasal carriage.