The choice of antibiotics for sinusitis in children with cystic fibrosis (CF) is empirical or based on lower airway cultures, because sinus cultures are difficult to obtain. The aim of this study was to identify the main organisms cultured from CF children with chronic sinusitis, and to evaluate the concordance of concomitant sinus, oropharyngeal swab (OP), and bronchoalveolar lavage fluid (BALF) cultures. OP and BALF cultures were done preoperatively, and sinus cultures were obtained during clinically indicated sinus surgery. The genetic identity of the bacteria was compared if the same organisms were present in upper and lower airway cultures. In total, 45 paired sinus-BALF cultures from 31 patients were included. Twenty-four of these had matched OP cultures. The mean age of patients was 9.5 ± 4.3 years, and 19 patients were ΔF508 homozygous. Bacterial sinus infection was present in 96%, caused by S. aureus (49%), P. aeruginosa (42%), and H. influenzae (22%). The diagnostic accuracy of BALF or OP cultures was low in predicting sinus infection, particularly at younger ages. Positive and negative predictive values (PPV and NPV) of BALF for P. aeruginosa infection were 65% and 67%, and for S. aureus, 76% and 63%, respectively. Predictive values for OP cultures were similar. Bacterial species were the same in sinus and OP or BALF samples of 12 patients of these bacteria 83% showed genetic identity. We conclude that S. aureus is an important pathogen in pediatric CF sinusitis, and that BALF or oropharyngeal cultures are poor predictors for organisms present in the sinuses. Pediatr Pulmonol. 2006; 41:445–451. © 2006 Wiley-Liss, Inc.