<p>To perform mucociliary clearance, motile cilia covering the surface of the respiratory tract coordinate their beating motions to push mucus out of the upper airways. Ciliated cells cover about half of the available surface, and present disordered but globally correlated beating directions. This architecture is altered as a consequence of several respiratory diseases such as Primary Ciliary Dyskinesia or viral infections that ultimately impair mucociliary clearance. Here, we present multi-physics simulations of a tissue scale model of the airway epithelium. The model reproduces the ciliated layer at individual cilium resolution, with physiological cilium beating shape, density and patchy distribution, in presence of an explicit mucus layer. We show how the spatial alignment of ciliated patches, their beating directions, and typical pathological conditions like cilia loss and immotility affect the beating coordination and the transport of mucus. While spatial disorder has a minor impact on the efficiency of mucociliary clearance, a detrimental effect is caused by the misalignment of the beating directions, cilia loss and immotility, as typical of several diseases. Our results provide a clear picture of the fluid mediated mucociliary clearance process in healthy and pathological conditions.</p><p></p>