Three transparent single cells, i.e., a cathode transparent single cell, an anode transparent single cell and an overall transparent single cell are tested and compared with a standard single cell. Results show the standard single cell presents the best performance and the overall transparent single cell shows the worst performance. This is because a large contact resistance exists between the gas diffusion layer and the graphite pierced flow field plate of a transparent single cell due to the deformation of the transparent flow field unit, which is caused by the bolt preload. Based on the testing data, four deformation process models are proposed to reveal how the structure differences affect the performance differences between the standard single cell and the transparent single cells. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.