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In this study three-dimensional computational model of a segment of bronchial airway surface liquid has been investigated to study the effect of various cilia abnormalities on mucociliary clearance (MCC), which was reported in common respiratory diseases. Numerical simulations have been devoted to studying a two-layer fluid model of the airway surface liquid (ASL) consisting of a Newtonian lower periciliary liquid (PCL) layer and a nonlinear viscoelastic upper mucus layer. The time-dependent governing and constitutive equations have been discretized and solved by a finite difference projection method on a staggered grid. The immersed boundary method has also been employed to study the effect of cilia propulsive effect on ASL. Numerical results have been devoted to investigating the influence of various cilia abnormalities, such as phase difference between cilia, cilia beat pattern, cilia beat frequency, cilia lattice geometry, missing cilia regions, and cilia density on MCC. The mucus was modeled as a nonlinear viscoelastic fluid in 3D geometry. Numerical results show that some cilia abnormalities such as cilia density, cilia beat pattern, and cilia beat frequency have a dominant effect on MCC and some abnormalities such as missing cilia regions and phase differences between cilia have a moderate influence on that. Results also show the negligible impact of cilia lattice geometry on mucus flow.