Results of molecular dynamics (MD) simulations on transport process of small molecules in amorphous cardo poly-etherether-ketone membranes, namely PEEK-WC, suffonated PEEK-WC and nitrated PEEK-WC are discussed. Atomistic simulations techniques have proven to be a useful tool for the understanding of structure-property relationships of materials and in particular MD can be used for detailed descriptions 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 occurring jump mechanism is characterised and visualised. Constants of diffusion and solubility coefficients have been calculated by the transition state Gusev-Suter Monte Carlo (MC) method.