Results of molecular dynamics (MD) simulations on transport and solubility of small molecules in amorphous cardo poly-ether-ether-ketone membranes are discussed. Atomistic simulation techniques have proven to be a useful tool for the understanding of structure-property relationships of materials. Although MD are still not an ideal tool for the quantitative prediction of gas permeation properties, this methodology can be used for a detailed description of the complex morphologies and transport mechanisms associated with rigid glassy structures. The diffusion process results from jumps of penetrant molecules between adjacent holes in the polymer matrix. The free volume and the occurring jump mechanism are characterized and visualized with different methods. Constants of diffusion and solubility coefficients have been calculated by the Transition State Gusev-Suter Monte Carlo method revealing a considerable agreement between simulated and calculated data.