BackgroundThe estimated prevalence of tracheobronchomalacia (TBM) in children is about 1:2100. Prevalence of intrathoracic malacia is higher in children with chronic lung disease such as bronchiectasis and cystic fibrosis (CF) and may contribute to increased morbidity.ObjectiveTo determine the prevalence and assess clinical features of tracheomalacia (TM), TBM and bronchomalacia (BM) in patients with primary ciliary dyskinesia (PCD).MethodsWe performed a retrospective case‐note review of all children with a confirmed or highly likely diagnosis of PCD attending Oslo University Hospital between 2000 and 2021. We selected those who had undergone flexible fiberoptic bronchoscopy (FB) and in whom the presence of TBM was assessed. We retrieved demographic and clinical data, including airway symptoms, PCD‐diagnostic criteria, indication for bronchoscopy, the presence of lobar atelectasis, microbiology and the descriptive and unblinded video‐recorded results of FB. Complications occurring during and after bronchoscopy were noted.ResultsOf 71 children with PCD, 32 underwent FB and were included in the review. The remaining 39 were included for TBM prevalence calculation only. Median age at FB was 6.0 years (3.1–11.9). Twenty‐two children (69%) had intrathoracic airway malacia. Four (13%) had isolated TM, seven (22%) had TBM, and 11 (34%) had isolated BM affecting either main (n = 4) or lobar bronchi (n = 7) (LBM), including four with associated lobar atelectasis. FB related complications, one major, 12 minor, were documented in 13 children (41%).ConclusionWe found a high prevalence of TBM among children with PCD undergoing FB. This may represent a significant comorbidity and have implications for patient management.