A convenient and efficient method for the site-directed incorporation of aldehydes generated on the oligosaccharide moieties at the C-terminal of immunoglobulin (IgG) using NaIO4 oxidation reaction is explored as a means of ensuring controlled assembly of IgG antibodies onto aminopropyltriethoxylsilane (APTES) derivatized silicon wafer surfaces. The orientation and antigen binding capacity (AgBC) of site-directly assembled IgG antibodies on derivatized surfaces were investigated using atomic force microscopy (AFM) and enzyme immunoassay (EIA), respectively. A major difference in preferential orientation is observed when the incubation of derivatized surfaces with oxidized IgG molecules is compared in two different kinds of buffer solutions. We obtained the stable and homogeneous IgG layer without loss of the AgBC on the APTES derivatized surface using the controlled incubation condition.