In this study, we synthesised specific filtration cartridges with selective recognition sites for target molecules and used them to separate interferon α-2b from aqueous solutions. We combined molecular imprinting technology with cryogel to achieve specific and rapid filtration of interferon α-2b through the macroporous structure of a cryogel network. Recombinant interferon α-2b-imprinted poly(2-hydroxyethyl methacrylate-N-methacryloyl-L-tryptophan) P(HEMATrp)/α-2bIFN cryogels were synthesised via free-radical bulk polymerisation under partially frozen conditions. The interferon α-2b filtration conditions were subsequently optimised with respect to factors such as pH, initial concentration, temperature, centrifugation speed, salt concentration and type and the amount of precomplex incorporated. Selectivity experiments were conducted in respect to isoelectric point as well as size of the competitor proteins under both uncompetitive and competitive conditions. The relative selectivity coefficients of the specific filtration cartridge in respect to isoelectronic points for interferon/IgG, interferon/HSA and interferon/insulin pairs were 3.72, 7.10 and 10.68 times greater than the coefficient of a non-imprinted [P(HEMATrp)] filtration cartridge, respectively. Similarly, the relative selectivity coefficients of the specific filtration cartridge in respect to competitor size for interferon/lysozyme, interferon/myoglobin and interferon/carbonic anhydrase pairs were calculated as 7.58, 10.40 and 11.68 under uncompetitive conditions whereas those values under competitive conditions were calculated as 1.08, 1.05 and 1.34, respectively. The results indicated that specific filtration cartridges developed could repeatedly adsorb interferon α-2b with a short separation time without any significant decrease in the adsorption capacity even if competitive conditions were conducted.