Self-assembled monolayers (SAMs) using various organic molecules were constructed on thin thermal silicon dioxide on silicon structures. These structures have potential bio-applications. The monolayers are part of a capacitor sensor based on the electrolyte-insulator-silicon (EIS) structure. The main goal of this work is to investigate the ability of SAMs for acting as an intermediate layer between aqueous solutions and silicon based biosensors. This work presents monolayers based on trimethoxy silanes with various functional groups such as: (a) (3-aminopropyl)-trimethoxysilane, (b) octadecyltrimethoxysilane and (c) trimethoxy(3,3,3-trifluoropropyl)silane. The biosensor is a differential sensor with a built in reference based on the structure of electrolyte-insulator-silicon or in ion-sensitive-field-effect-transistors (ISFETs). While the methyl and fluorine groups can act as the reference part, which is passive to the bio-molecules detection, the capacitor containing the amine groups has the sensing capabilities to the biological molecules. The amine (NH2) tail groups can be active for those attachments via glutaraldehyde. The film's study and characterization was made by spectroscopic ellipsometry, contact angle method (CA) and FT-IR spectroscopy. The electrical methods such as capacitance-voltage (C-V) and electrochemical impedance spectroscopy (IS) were used to investigate the whole electrolyte/SAM/SiO2/Si structure. We will show the detection capabilities of these 2D structures, its electrical equivalent model through a simulation fitting and will discuss the application of those structures to bio-sensitive metal/oxide/silicon (MOS) devices. (C) 2009 Elsevier Ltd. All rights reserved.