We present a study of the elution behaviour of polymers through a liquid chromatographic column and its dependence on the interactions with the substrate. An earlier method based on statistical thermodynamics is employed to describe chains in the presence of interacting cubic pores in terms of the probability to find the chains in and far from the pores. The partition coefficient of the chains between the mobile and the stationary phases, as a function of the polymer molecular weight, the average size of the pores and a polymer-substrate interaction parameter, is determined and compared with the results of supportive experiments. Two series of chromatographic experiments with two columns with substrates different in nature but with the same pore size, indisputably shows the importance of the polymer-surface interactions. Due to the change of the nature of the substrate an alternation of the mode of elution of the same poly(methyl methacrylates) in the same solvent is observed.