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RATIONALE Dynamic collapse of the tracheal lumen (tracheomalacia) occurs frequently in premature neonates, particularly those with common comorbidities such as bronchopulmonary dysplasia. The tracheal collapse increases the effort necessary to breathe (work of breathing, WOB). However, quantifying the increased WOB related to tracheomalacia has previously not been possible. Therefore, it is also not currently possible to separate the impact of tracheomalacia on patient symptoms from parenchymal abnormalities. OBJECTIVES To measure the increase in WOB due to airway motion in individual subjects with and without tracheomalacia and at different levels of respiratory support. METHODS Fourteen neonatal intensive care unit subjects not using invasive mechanical ventilation were recruited. Eight were diagnosed with tracheomalacia via clinical bronchoscopy, and six did not have tracheomalacia. Self-gated 3D ultrashort echo time MRI was performed on each subject with clinically-indicated respiratory support to obtain cine-images of tracheal anatomy and motion during the respiratory cycle. The component of WOB due to resistance within the trachea was then calculated via computational fluid dynamics (CFD) simulations of airflow based on the subject's anatomy, motion, and respiratory airflow rates. A second CFD simulation was performed for each subject with the airway held static at its largest (i.e. most open) position, to determine the increase in WOB due to airway motion and collapse. RESULTS The tracheal resistive component of WOB was increased due to airway motion by an average of 337% ± 295% in subjects with tracheomalacia and 24% ± 14% in subjects without tracheomalacia (p < 0.02). In the tracheomalacia group, subjects who were treated with continuous positive airway pressure (CPAP) using RAM cannula expended less energy for breathing compared to the subjects who were breathing room air or on high flow nasal cannula. CONCLUSIONS Neonatal subjects with tracheomalacia have increased energy expenditure compared to neonates with normal airways and CPAP may be able attenuate the increase in respiratory work. Subjects with tracheomalacia expend more energy on the tracheal resistive component of WOB alone than previously reported values in non-trachomalacia patients for the resistive WOB in the entire respiratory system. CFD may be able to provide an objective measure of treatment response for children with tracheomalacia.