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Methods for characterization of epoxy-functionalized substrates used for microarray applications, prepared by silanization with 3-glycidoxypropyltrimethoxysilane, have been developed. Contact angle measurements, X-ray photoelectron spectroscopy, time of flight secondary ion mass spectrometry and fluorescence based methods have been applied to investigate these epoxy-functionalized microarray substrates. The surface density of epoxy-functionalized glass slides was investigated by fluorescence labeling of surface species utilizing Rhodamine 110 as fluorescence probe.