Nowadays, interventions associated with the implantation of tracheal prostheses in patients with airway pathologies are very common. This surgery may promote problems such as migration of the prosthesis, development of granulation tissue at the edges of the stent with overgrowth of the tracheal lumen or accumulation of secretions inside the prosthesis. Among the movements that the trachea carries out, swallowing seems to have harmful consequences for the tracheal tissues surrounding the prosthesis. In this work, a finite-element-based tool is presented to construct patient-specific tracheal models, introducing the endotracheal prosthesis and analysing the mechanical consequences of this surgery during swallowing. A complete description of a patient-specific tracheal model is given, and a fully experimental characterization of the tracheal tissues is presented. To construct patient-specific grids, a mesh adaptation algorithm has been developed and the implantation of a tracheal prosthesis is simulated. The ascending deglutition movement of the trachea is recorded using real data from each specific patient from fluoroscopic images before and after implantation. The overall behaviour of the trachea is modified when a prosthesis is introduced. The presented tool has been particularized for two different patients (patient A and patient B), allowing prediction of the consequences of this kind of surgery. In particular, patient A had a decrease of almost 30 per cent in his ability to swallow, and an increase in stresses that were three times higher after prosthesis implantation. In contrast, patient B, who had a shorter trachea and who seemed to undergo more damaging effects, did not have a significant reduction in his ability to swallow and did not present an increase in stress in the tissues. In both cases, there are clinical studies that validate our results: namely, patient A underwent a further intervention whereas the outcome of patient B's surgery was completely successful. Notwithstanding the fact that there are a lot of uncertainties relating to the implantation of endotracheal prostheses, the present work gives a new insight into these procedures, predicting their mechanical consequences. This tool could be used in the future as pre-operative planning software to help thoracic surgeons in deciding the optimal prosthesis as well as its size and positioning.