The wettability of the surfaces inside the microchannels of a microfluiclic device is an important property considering a liquid flows through them. Contact angle measurements usually applied to test the wettability of surfaces cannot be used for an analysis of microchannel walls within microfluiclic devices. A workaround is the use of surface analytical methods, which are able to reach points of interest in microchannels and may provide information on the surface chemistry established there. In calibrating these methods by using flat polymer wafers, where the contact angle can be measured as usual, data measured in real microchannels can be evaluated in terms of wetting properties. Reference wafers of bisphenol-A polycarbonate, a polymeric material that is often used in fluidic microdevice fabrication, were treated under different oxygen plasma conditions. The modified surfaces were characterized by using XPS, time of flight (ToF)-SIMS and atomic force microscope (AFM). Surface chemistry and surface topography have been correlated with contact angle measurements. In addition, effects of ageing or rinsing after plasma treatment have also been investigated. Copyright (C) 2008 John Wiley & Sons, Ltd.