Silanization protocols for glass slides and silicon oxide substrates usually include acid rinsing steps to activate the surfaces prior to silanization. In our group, field-effect transistor devices and electrolyte-insulator-semiconductor structures are used to electronically record signals from cells or to detect biomolecular interactions at the solid-liquid interface. A miniaturized, high sensitive, field-effect-based semiconductor device should expose at its input stage just a thin oxide (< 10 nm) to the electrolyte solution. Therefore, silanization protocols are needed, which do not alter the thin oxide layers in terms of topology changes or thickness loss. In this article we evaluated different protocols for wet cleaning and activation of thin silicon oxides. The efficiency of the cleaning methods was verified with Contact Angle Measurements, Atomic Force Microscopy, and Fourier-Transform Infrared Spectroscopy. Furthermore, X-ray Photoelectron Spectroscopy was used to characterize the oxides after the cleaning and silanization procedures. (3-aminopropyl)triethoxysilane was used to functionalize the oxide surfaces for further attachment of biological molecules (e.g. proteins, DNA). Thicknesses and uniformity of the silane coatings were evaluated by Imaging Ellipsometry. (c) 2005 Elsevier B.V. All rights reserved.