For the clarification of water transport mechanisms in operating fuel cells, synchrotron radiation computed tomography (SR-CT) was applied. A novel fuel cell has been designed that exposes the entire active area (7 mm(2)) to the SR beam while at the same time allowing for full fuel cell operation during the imaging experiment. This micro fuel cell has been qualified successfully prior to the SR imaging experiments. The cell voltage was 600 mV at 0.2 A cm(-2) (open circuit voltage, OCV > 950 mV) and the operation was stable for hours. However, under SR beam exposition for in situ imaging, severe cell performance degradation within minutes has been reproducibly observed. Even after the SR beam had been switched-off cell operation remained irreversibly degraded whilst OCV could be recovered. Preliminary results indicate a higher degradation sensitivity of the cathode side of the cell. Apparently, the unique setup of the experiment which exposes an operating fuel cell with the entire active area to the SR beam reveals otherwise unnoticeable degradation mechanisms. It may have to be concluded that the very same materials degrade heavily during beam exposure that are subject of the imaging investigation. Consequently, the applicability of SR imaging to study water transport in porous fuel cell materials has to be revisited critically. This publication describes the observations made during fuel cell operation under SR beam exposure and discuss potential mechanisms that may cause beam-induced performance degradation. (C) 2010 Elsevier B.V. All rights reserved.