Permeability of virtual cement seems to exceed experimental data by several orders of magnitude. The difference may not be that dramatic, since samples are in practise not always fully saturated as generally assumed. This has enormous effects on permeability. Therefore, a numerical study is conducted on water and gas permeability of partly saturated cement paste based on simulated microstructures. The results show that water permeability declines with the decreasing saturation degree. A similar but inverse relationship exists between gas permeability and saturation degree. The changes of pore size distribution and pore connectivity will be discussed in this paper. The results in terms of relative water and gas permeability have been validated against lattice Boltzmann simulations and experimental data, respectively. A satisfactory agreement is found.