Background: Primary ciliary dyskinesia (PCD) is associated with ventilation defects and heterogeneous impairment of pulmonary function. Spirometry may underestimate PCD severity and complexity. This study aimed to evaluate spirometry, lung clearance index (LCI), and impulse oscillometry (IOS) in children with PCD and healthy controls, and compare them in terms of early detection of lung disease. Methods: In this cross-sectional, prospective study, participants included children aged 6-18 years with PCD and healthy age-matched controls. Lung function tests using LCI, IOS, and spirometry were conducted on the same day for all participants. Results: Thirty-two children with PCD (median age 13.19 years) and 44 age-matched healthy controls (median age 12.32 years) were studied. PCD was associated with lower FEV1, FVC, FEV1/FVC, R5, R10, R15, R20, X5, Fres, and LCI 2.5% mean values (p<0.05). Abnormal LCI 2.5% was found in 46.5% of patients with predicted FEV1 > 80%. Significant inverse correlations were observed between LCI 2.5%, FEV1, FVC, and Fres in PCD patients (p<0.001, r:-0.635; p=0.002, r:-0.517; p=0.006, r:-0.479; respectively. Conclusion: This is the first study to compare LCI, IOS, and spirometry in children with PCD. The study has shown that there are significant differences in spirometry, LCI, and IOS values between children with PCD and healthy controls. LCI can detect airway anomalies earlier than spirometry in PCD patients. IOS and LCI are valuable respiratory function tests that can be used in PCD follow-up.