Purpose: To estimate the effect of the number of computed tomography (CT) sections on trapped air (TA) assessment in patients with cystic fibrosis (CF) by using an established scoring system and a new quantitative scoring system and to compare CT and pulmonary function test (PFT) estimates of TA in a cross-sectional and longitudinal study.Materials and Methods: In this institutional review board-approved pilot study, 20 subjects aged 6-20 years (12 female and eight male; median age, 12.6 years) contributed two expiratory CT studies (three-section baseline CT, volumetric follow-up CT) and two PFT studies over 2 years after parental informed consent was obtained. From follow-up CT studies, seven sets were composed: Set 1 was volumetric. Sets 2, 3, 4, and 5, had spacing of 2.4, 4.8, 9.6, and 20.4 mm, respectively, between sections. Sets 6 and 7 contained five and three sections, respectively. Longitudinal follow-up was performed with three sections. All images were deidentified and randomized, and TA was scored with the Brody II system and a new quantitative system. Statistical analysis included the Wilcoxon signed rank test, calculation of Spearman and intraclass correlation coefficients, and use of three-section and linear mixed models.Results: For the Brody II system, the intraclass correlation coefficient for set 1 versus those for sets 2 through 7 was 0.75 versus 0.87; however, mean scores from sets 6 and 7 were significantly lower than the mean score from set 1 (P = .01 and P <.001, respectively). For the quantitative system, the number of sections did not affect TA assessment (intraclass correlation coefficient range, 0.82-0.88; P > .13 for all). CT and PFT estimates were not correlated (rs = 20.19 to 0.09, P = .43-.93). No change in TA over time was found for CT or PFT (P > .16 for all).Conclusion: The number of sections affected Brody II estimates, suggesting that three-section protocols lead to underestimation of TA assessment in patients with CF when using the Brody II system; CT and PFT estimates of TA showed no correlation and no significant change over time.