The development of rapid analysis of human serum for the presence of allergen-specific IgE is currently important. Consequently, we developed two types of 3D protein biochips. The first one is a 3D hydrogel biochip containing hydrogel droplets with protein molecules (allergens, immunoglobulins and others). These droplets are disposed on elements consisting of short polymer brushes grafting from a surface of polybutylene terephthalate polymer. The immobilization of proteins was induced by short-wave UV radiation. On such a biochip, the kinetics of allergen-sIgE complex formation reached 70% of saturation for 6 hours. Also we developed a 3D brush microchip containing on the surface of a polyethylene terephthalate polymer the brush elements with protein molecules covalently immobilized by opening oxirane cycles by amino and thiol nucleophilic groups contained in proteins. In the case of 3D brush microchip the kinetics of allergen-sIgE complex formation reached 100% of saturation for 3 hours, and fluorescent signals were 2-3 times higher than those of the 3D hydrogel biochip. Thus, the comparative analysis revealed that 3D brush biochips are more useful for further studies of protein-protein interactions than 3D hydrogel ones.