Pore-scale simulations of two phase flows in a packed-sphere bed and in a carbon paper gas diffusion layer (GDL) are carried out using the free energy multiphase lattice Boltzmann method (LBM). The simulations are performed based on the detailed microstructure of the porous media under periodic boundary conditions such that the average phase saturations in the porous medium remain constant. A comparison of the simulated and measured relative permeabilities for the packed sphere bed as a function of non-wetting phase saturation is performed. and effects of the wettability and the anisotropic characteristics of relative permeabilities of the GDL are investigated. (C) 2009 Elsevier Ltd. All rights reserved.