A new molecular imprinting technique using covalently immobilized hemoglobin (Hb) is described for creating Hb-specific recognition cavities on silica. Two kinds of organic silane (3-aminopropyltrimethoxysilane: APTMS, and trimethoxypropylsilane: TMPS) were polymerized on a surface of porous silica after the Hb template was covalently immobilized by forming imine bonds, and their influence was analyzed. The results showed that not only the silane amount but also the relative proportions play an important role in protein imprinting. Pore size distribution on Hb imprinted silica was determined by nitrogen adsorption/desorption after removing the template Hb. The Hb-imprinted silica using covalently immobilized Hb (MIPi) as a template proved superior to silica using free Hb (MIPf) regarding displacement of template Hb, and selective re-adsorption as compared with other non-template proteins. The results suggested the capacity for selective adsorption of MIPi to be not only based on the isoelectric point (pI) and protein molecular weight, but also the characteristics of protein recognition cavities imprinted on base silica.