In tracheo- and bronchomalacia, localisation and determination of collapse is necessary for planning of surgical procedure. We compared inspiratory and expiratory spiral CT, cine CT, bronchoscopy, exemplary cine MR, and evaluated the clinical relevance. Twenty-nine patients (2 follow-ups; mean age 61 years, age range 27-85 years) with suspected or verified tracheal stenosis or collapse (post-tracheotomy: n = 17; neoplasm: n = 5; other: n = 7) underwent paired breath-hold inspiratory and expiratory spiral CT. Forty-five additional cine CT were performed at 1-4 levels (mean 1.5) during continuous respiration (increment 100 ms) to clarify respiratory collapse. The tracheal cross-sectional diameters of both techniques were calculated. Comparison with bronchoscopy, follow-up, and influence upon therapy were evaluated retrospectively. Exemplary comparison with cine MR (8 frames/s) was done in 3 cases. In addition to bronchoscopy, further information concerning localisation, extent, collapse, stability of the tracheal wall, distal portions of the stenosis and extraluminal compressions were obtained. A significantly higher degree and more pathological collapses (> 50%) were seen using cine CT (38%) compared with paired spiral CT (13%; degree: p < 0.0001; number: p < 0.001). The findings changed the further therapeutic procedure in 16 of 29 patients. Further stenoses were excluded and bronchoscopy was verified in another 13 of 29. Temporal resolution of cine CT and cine MR is sufficient; however, spatial resolution of cine MR is inferior. Paired inspiratory and expiratory spiral CT localises tracheal stenoses and demonstrates relevant extraluminal compression. Significantly improved evaluation of respiratory collapse and further information of localised tracheal instability is obtained by cine CT. Cine MR promises more functional information especially due to free choice of imaging plane.