Rationale: Primary ciliary dyskinesia (PCD) is an inherited disorder characterized by heterogeneous airway disease. Traditional lung function techniques (e.g., spirometry) may underestimate severity and complexity of PCD. Objectives: We assessed lung impairment in individuals with PCD using structural and functional magnetic resonance imaging (MRI) and different lung function techniques. Methods: A total of 30 study participants with PCD (median, 13.4 yr; range, 5-28 yr) underwent structural and functional MRI, spirometry, and multiple breath washout (MBW) on the same day. Primary endpoints included structural MRI morphology scores, relative ventilation, and perfusion impairment from functional MRI, forced expiratory volume in 1 second (FEV1) from spirometry, and lung clearance index (LCI) from MBW. Results: Severity and complexity of PCD lung disease varied significantly between individuals. Structural lung disease was detected in all subjects with a median (interquartile range) extent score of 10.3 (7-19; maximum score = 60). Functional MRI ventilation impairment was present in 52% of subjects, affecting 24.2% (21.1 to 25.2%) of the lung. Relative perfusion impairment was detected in 78% of individuals affecting 21.1% (19.4 to 25.9%) of the lung. LCI was abnormal in 83% (median, 8.3 [2.6 to 13.2] z-scores) and FEV1 was abnormal in 27% (20.5 [21.6 to 0.3] z-scores) of individuals. Concordance between spirometry and imaging outcomes was poor, with 52% of patients showing both abnormal MRI and LCI values, but normal FEV1. Conclusions: Discordance between lung function and imaging outcomes in patients with PCD supports the use of both imaging and lung function, such as MBW, for surveillance of this heterogeneous disease.