Cystic fibrosis (CF) is the most common life-restricting, genetically inherited disease among Caucasians affecting approximately 30,000 people in the United States. Lung disease is the major cause of morbidity and mortality in CF. A number of oral, inhaled, and intravenous therapies are available to combat CF lung disease. Of these, this research project focused on inhaled dornase alfa, oral azithromycin, inhaled tobramycin, and inhaled aztreonam. Data to address three research aims were requested and obtained from the Cystic Fibrosis Foundation Patient Registry (CFFPR). The first aim examined the use of inhaled dornase alfa in younger children with CF. With no clinical efficacy data of dornase alfa in children ≤ 6 years of age, the study utilized subsequent forced expiratory volume in 1 second (FEV₁) measured between 6 - 7 years of age, to assess the effectiveness of long-term dornase alfa use ≤ 6 years of age. Propensity score methods were used to reduce the likelihood of treatment indication bias. The results suggested that receiving treatment with dornase alfa before 6 years of age did not improve FEV₁ between 6 - 7 years. Unmeasured covariates leading to treatment indication bias were likely one of the key explanations for these results. Additionally, lack of a more sensitive outcome than FEV₁ to assess lung function in young patients with early lung damage was thought to be another reason for the failure to reject the null hypothesis. The second aim assessed the long-term clinical effectiveness of chronic azithromycin use on the rate of FEV₁ decline in CF patients between 6 - 20 years of age. This study was novel in that the rate of FEV₁ decline, rather than change in FEV₁ from baseline, was the primary outcome, which was characterized using propensity score matching followed by a linear mixed model analysis. The results of the analysis suggested that the rate of FEV₁ decline was slower in patients who did not receive chronic treatment with azithromycin. Treatment indication bias was thought to play an important role in the direction of the association between treatment and outcome. Associations between FEV₁ % predicted and many of the other study variables included in the analysis were consistent with previous studies. The final aim compared the clinical effectiveness of a combination of inhaled tobramycin and aztreonam with inhaled tobramycin alone on the rate of FEV₁ decline in CF patients between 6 - 20 years of age. This aim was novel in that the effect of this combination treatment on rate of decline in FEV₁ has never been assessed. A linear mixed model analysis was used after matching patients in the two treatment groups on their propensity scores. Once again, the results were contrary to the alternative hypothesis with the combination group having a steeper rate of FEV₁ decline than the group that was treated with tobramycin alone. An important reason for this result was thought to be unresolved treatment indication bias that could not be eliminated even with the use of the propensity score methods used to test the associated hypothesis. The use of validated methods of analysis, i.e., propensity scores, to counter treatment indication bias using the largest available observational dataset for CF, was one of the key strengths of this study. Moreover, this study highlighted important weaknesses in the CFFPR with regards to lack of data on patient and physician-level variables - an area of active interest for the Cystic Fibrosis Foundation.