In this contribution, the possibilities and limits of atomic force microscopy (AFM) for investigation of fuel cell component degradation are evaluated. In particular the adhesion force and dissipation energy of the surface measured by a material sensitive AFM technique - the HarmoniX-mode (Bruker Corp.) - have been used as a measure for the relative polytetrafluoroethylene (PTFE) content of surfaces and could be quantified by calibrating with sample of known composition. Differently operated samples with microporous layers (MPLs) of commercial gas diffusion layers (GDLs) were investigated before and after operation and were compared to artificially aged and reference samples. A larger degradation of the cathode material compared to the anode was always found. As an additional example for the potential of AFM and infrared absorption spectroscopy (FTIR-ATR) the local PTFE content of a cell with a segmented anode flow field has been investigated. The results of PTFE loss at MPL and electrode surfaces from AFM measurements and infrared spectroscopy delivered different results which were explained by the distinct information depth of both methods. The large relative differences of PTFE content of the different segments were correlated with the mechanical properties of the special design of the segmented cell. (C) 2011 Elsevier B.V. All rights reserved.