The aim of this study was the oriented immobilization of IgG molecules on the silicon surfaces. A multiple-step procedure was applied for oriented immobilization of IgG in this study. After hydroxylation of the Si(001) surfaces, 3-glycidoxypropyltrimethoxysilane (GPTS) molecules were self-assembled onto these substrates. Dipping time and GPTS concentration were found to be effected by on both layer thicknesses and water-contact angles. 2,2'-(ethylenedioxy)diethylamine (EDA) molecules were then covalently attached to the silicon surface with GPTS molecules. There was no effect of concentration on the formation of EDA molecules on the surfaces, while EDA deposition increased with the dipping time significantly. Imaging ellipsometry and atomic force microscopy (AFM) images exhibited aggregate formation at this step. Protein-A molecules were bound to the free amino groups of EDA molecules on the substrate surface, especially onto the aggregates by using a carbodiimide (i.e., EDAC) as the activating agent. We were able to immobilize IgG molecules in an oriented form onto the protein-A attached surfaces, especially in the regions, where EDA aggregates are located.