In the past years, transport of gases in clay buffer materials for Engineered Barrier Systems (EBS) has been deeply investigated by many research programs in the field of nuclear waste disposal. The phenomenological features of gas transport obtained from experimental tests have been used to define modelling approaches to interpret gas-induced effects in bentonite buffer material. The aim of these models is to analyze the perfor-mance of clay buffer materials in a long term nuclear waste disposal scenario. The gas transport phenomenon is strongly influenced by the microstructural features of the bentonite. In this paper, an advanced finite element approach is used to simulate the gas migration phenomena in the framework of stochastic finite element analy-sis. This tool highlights the most relevant factors affecting the accuracy of the modelling process to improve model efficiency and to estimate the simulation uncertainties. The approach highlights the need of an accurate microstructural characterization of bentonite to define the water retention behavior and the hydraulic response of the buffer material.