Macroporous monolithic columns with different mean pore size (from 360 to 2020 nm) and appropriate flow-through properties were synthesized using free radical in situ copolymerization of glycidyl methacrylate, 2-hydroxyethyl methacrylate and ethylene dimethacrylate. In order to predict the composition of porogen mixture to generate the pores in the interested size interval, the Hildebrand theory was used. Ribonuclease A and its specific low- and macromolecular substrates cytidine-2′,3′-cyclic monophosphate sodium salt and RNA were applied as model system. The effect of mean pore size of macroporous monoliths used for enzyme immobilization on molecular recognition and biocatalytic characteristics was examined. The monitoring of RNA degradation was performed using anion-exchange HPLC on monolithic CIM DEAE analytical column. The high efficiency of heterogeneous biocatalysts obtained comparatively to the catalytic reaction of RNA degradation in solution was demonstrated. Additionally, the series of six monolithic immobilized enzyme reactors with different amount of biocatalyst was prepared and studied regarding to the biocatalytic properties at recirculation mode at two experimental variants, e.g. (i) fixed range of concentrations of circulated substrate solutions, and (ii) fixed range of substrate/enzyme molar ratios.