It is known that aminosilanized Si wafers may be used as microarray platforms. Results of an XPS study of a cleaning applied to Si wafers prior to aminosilanization are presented and discussed. Furthermore, the results of an aminosilanization protocol optimized in terms of nitrogen chemistry are described. After optimization of the protocol a free amine content of 94% was reached. The surface chemistry was investigated in this study by using XPS, time of flight (ToF)-SIMS and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Reference to aminosilanization protocols reported in the literature has been made. Copyright © 2008 John Wiley & Sons, Ltd.