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Usually hydroxyl groups present on top of oxidized silicon served as binding centers for a silanization reaction toward surface functionalization. In this study, we developed a novel surface functionalization strategy where hydroxyl functionalization on nonoxidized silicon surfaces are obtained. These surfaces were stable for several weeks even in ambient air at room temperature. This high stability indicates a strong spatial isolation of the hydroxyl groups because they keenly tend to undergo a condensation reaction, forming silicon oxide. To prove the applicability of the obtained hydroxylated silicon surface, we further modified the hydroxyl groups with a commonly used silane molecule, (3-aminopropyl)triethoxysilane (APTES). The functional amino groups of the APTES layer bonded to the surface were subsequently altered by N -maleoyl-β-alanin to generate a surface highly specific for the immobilization of thiol-containing biomolecules (like thiolated single-stranded DNA or cysteine-tagged proteins). All modification steps have been investigated by IR spectroscopic ellipsometry measurements.