Gas transport in non-woven gas diffusion layers of a high-temperature polymer electrolyte fuel cell was calculated with the Lattice Boltzmann method. The underlying micro structure was taken from two sources. A real micro structure was analyzed in the synchrotron under the impact of a compression mask mimicking the channel/rib structure of a flow field. Furthermore a stochastic geometry model based on synchrotron X-ray tomography studies was applied. The effect of compression is included in the stochastic model. Gas transport in these micro structures was simulated and the impact of compression was analyzed. Fiber bundles overlaying the micro structure were identified which affect the homogeneity of the gas flow. There are significant deviations between the impact of compression on effective material properties for this type of gas diffusion layers and the Kozeny-Carman equation.