Green vehicles that employ proton-exchange membrane (PEM) fuel cells as the power source of their propulsion systems have been developed to an advanced stage in recent years. Nevertheless, additional fundamental studies are required for further development of PEM fuel cells. Anisotropy of carbon paper microstructures can greatly affect the water droplet behavior through the porous gas diffusion layers (GDLs) of these fuel cells; this is investigated in the current paper for the first time. For performing such an investigation, the movement of three different water droplets with three dissimilar radiuses through three carbon paper GDLs with three dissimilar anisotropy levels has been analyzed by several three-dimensional (3D) lattice Boltzmann simulations. The analysis results illustrate that for water droplets with smaller initial radiuses (15 or 20 mu m) increasing the microstructure anisotropy level (i.e., making carbon fibers more in-plane aligned) makes droplet ejection faster. However, for water droplets with larger initial radiuses (25 mu m), increasing the anisotropy level does not assist water droplet removal from the GDL.