Recently, time-of-flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy (XPS) instrumentation has been used to address areas of interest within micro-fluidic devices providing full access to the surface chemistry established at the bottom of micro-channels therein. After careful calibration, information on surface chemistry as obtained by ToF-SIMS or XPS can be interpreted in terms of wettability expressed as contact angles which are then characteristic for the inner walls of micro-channels. Standard contact angle measurement is not applicable in micro-channels. The approach has been demonstrated to be successful with two different micro-fluidic devices hot embossed into high-end quality poly(methyl methacrylate) (PMMA) or Polycarbonate wafers. A pre-selected surface chemistry at micro-channel walls can be established by plasma technologies but ageing and rinsing effects have to be under control. A combination of ToF-SIMS, XPS and contact angle measurement techniques has been demonstrated to provide the required information. Finally, it is shown by ToF-SIMS and XPS analysis that in the production of micro-fluidic parts during practical processing using hot embossing technologies, material originating from cover foils will reside on the polymer wafer's surface. Moreover, residues of releasing agents as silicone oil used during processing can be detected by ToF-SIMS. Both cover foil residues and silicones are issues of trouble shooting in micro-fluidics because they will change contact angles efficiently. Copyright (C) 2010 John Wiley & Sons, Ltd.