OBJECTIVES: This study compared the relative cost-effectiveness of daily recombinant human deoxyribonuclease (rhDNase), with alternate day rhDNase and hypertonic saline (HS) for treating children with cystic fibrosis (CF). METHODS: A randomized controlled trial with a crossover design allocated 40 CF children consecutively to 12 weeks of daily rhDNase, alternate day rhDNase, or HS. The primary outcome measure was forced expiratory volume in 1 second (FEV1), a measure of lung function. All health resource use was prospectively documented for each patient and multiplied by unit costs to give a total health service cost for each 12-week treatment period. The nonparametric bootstrap method was used to present cost-effectiveness acceptability curves and net benefit statistics for each treatment comparison, for various hypothetical levels of the decision maker's ceiling ratio. RESULTS: Compared with HS, there was a 14% improvement in FEV1 for daily rhDNase (95% Cl, 5% to 23%), and a 12% improvement (95% Cl, 2% to 22%) for alternate day rhDNase. For a ceiling ratio of 200 pounds sterling per 1% gain in FEV1, the mean net benefits of daily and alternate day rhDNase compared with HS were 1,158 pounds sterling (95% Cl, -621pounds sterling to 2,842) and 1,188 pounds sterling (95% Cl, -847 to 3,343), respectively; the mean net benefit of daily compared with alternate day rhDNase was -30 pounds sterling (95% Cl, -2,091 pounds sterling to 1,576). CONCLUSIONS: If decision makers are prepared to pay 200 pounds sterling for a 1% gain in FEV1 over a 12-week period, then on average either rhDNase strategy is cost-effective.