In present work, the development of macroporous monolithic layers bearing the artificial recognition sites toward L-phenylalanine has been carried out. The set of macroporous poly(2-aminoethyl methacrylate-co-2-hydroxyethyl methacrylate-co-ethylene glycol dimethacrylate) materials with average pore size ranged in 340–1200 nm was synthesized. The applicability of Hildebrand's and Hansen's theories for the prediction of polymer compatibility with porogenic solvents was evaluated. The dependences of average pore size on theoretically calculated parameters were plotted. The linear trend detected for Hansen's theory has indicated the high suitability of this approach to select appropriate porogens. The synthesized monolithic MIP layers were tested toward the ability to rebind phenylalanine-derivative in microarray format. The influence of such factors as average pore size of the material, the concentration of template molecule in polymerization mixture, interaction time of analyte with its imprinted sites on binding efficiency were studied. The developed materials demonstrated good analyte rebinding from buffer solution with recognition factors 2.5–3.4 depending on the MIP sample. The comparable rebinding efficiency was also detected when the analysis was carried using complex biological media. The selectivity of phenylalanine binding from the equimolar mixture of structural analogues was 81.9% for free amino acid and 91.2% for labeled one.