Background and Objectives Functional and structural lung evaluations are part of the follow-up of patients with primary ciliary dyskinesia (PCD). We aimed to evaluate transversal and longitudinal relationships between lung function test (LFT) and chest computed tomography (CT) in children with PCD, in stable clinical condition. Materials and Methods Data from children followed in the French National Center were retrospectively collected. Inclusion criteria were (i) definitive diagnosis of PCD, (ii) age less than 15 years at the beginning of follow-up, (iii) at least 8 years of follow-up, (iv) at least two couples of concurrent CT and LFT available in a phase of clinical stability of the lung disease without modification of the treatment regimen in the last 4 weeks. Twenty children (median age at entry 4.6 years, median follow-up 15.4 years) were included. Concurrent LFT (blood gas and spirometry) and CT (score) results were recorded. Results LFT indices (PaO2 (n = 210), FVC, FEV1, FEF2575% (n = 195)) significantly decreased with age, and the mean annual decrease (z-score (% predicted)) was −0.17 (−0.49%), −0.09 (−0.50%), −0.10 (−0.89%), and −0.07 (−1.73%), respectively. First CT (median age 8.7 years) revealed bronchiectasis (70%), mucous plugging (70%), peribronchial thickening (90%), parenchymal abnormalities (65%), and hyperinflation (50%). CT scores (n = 74) significantly increased with age, and was negatively correlated to PaO2, FVC, FEV1, and FEF2575% longitudinal changes. Conclusion In stable clinical condition, functional, and structural progressive impairments significantly correlated in children with PCD. Further prospective studies, including large populations of patients with various levels of disease severity, are needed to confirm whether lung function follow-up can be used to adjust CT frequency and help at minimizing the radiation burden in children with a good life expectancy. Pediatr Pulmonol. 2012. 47:816–825. © 2012 Wiley Periodicals, Inc.