Background Accelerated lung function decline in cystic fibrosis (CF) is associated with mucoid Pseudomonas aeruginosa infection. Recent data suggest that mucoid P. aeruginosa may amenable to elimination from the airway. We aim to determine whether the initiation of an aggressive antibiotic eradication regimen upon initial discovery of mucoid P. aeruginosa in the CF airway could be successful in clearing the organism from the CF lung. Methods We performed a retrospective analysis of patients with CF who demonstrated new growth of mucoid P. aeruginosa in an airway culture between January 2003 and December 2008. The primary endpoint was clearance of mucoid P. aeruginosa, based upon the Leeds criteria, with no further growth of mucoid P. aeruginosa cultures within 12 months of the initial discovery and treatment. Factors associated with successful clearance were also evaluated. Results Forty-eight of 355 patients with CF had a new diagnosis of mucoid P. aeruginosa during the study period; 15 patients underwent an eradication attempt, while 33 patients received no increase in therapy. We observed clearance of mucoid P. aeruginosa in 73.3% of patients undergoing an eradication attempt, whereas 36.6% of those that did not undergo attempted eradication cleared the organism at 1 year (P < 0.05). Prolonged mucoid P. aeruginosa airway clearance (>24 months) for mucoid P. aeruginosa was seen in 60.0% in subjects undergoing eradication compared to 21.2% (P = 0.02) in control patients. At the study conclusion, lung function was greater in subjects who underwent an eradication attempt than in patients who did not undergo an eradication attempt (FEV1%: 91.7% vs. 75.0%, P = 0.04). Conclusions Clearance of initial mucoid P. aeruginosa from the airways of select patients with CF is possible with current antibiotic regimens, and the attempt may be associated with improved lung function. Pediatr Pulmonol. 2012. 47:1113-1122. © 2012 Wiley Periodicals, Inc.