Molecular modeling has become a useful and widely used tool to predict diffusion coefficients of molecules adsorbed in the pores of zeolites and other nanoporous materials. These simulations also provide detailed, molecular-level information about sorbate structure, dynamics, and diffusion mechanisms. We review recent advances in this field, including prediction of various transport coefficients (Fickian, Onsager, Maxwell-Stefan) for single-component and multicomponent systems from equilibrium and non-equilibrium molecular dynamics (MD) simulations, elucidation of anomalous diffusion effects induced by the confining pore structure, and prediction of slow diffusion processes beyond the reach of MD simulations.