The stacking modes of graphene oxide monolayers (GO) when forming thin films is a crucial aspect determining many properties especially those related with transport. Stacking, morphology and effects of thermal and chemical reduction are studied combining in-situ synchrotron radiation diffraction and atomic force microscopy with simulations. The GO flakes mimic the substrate morphology and present an almost perfect stacking for few-layer films (2-10 layers) when in-plane flake size is large enough. The interlayer distance is found to be 1 nm irrespective of the film thickness and drastic discontinuities upon thermal annealing are observed between 100 and 200 degrees C. Moreover, the short GO-GO distance (0.38 nm) observed at temperatures (500 degrees C) where oxygen content is still high indicates that stacking is mainly governed by embedded water molecules. The large interlayer distance (0.76 nm) in chemically reduced films and its robustness against thermal annealing are due to the folding of the edges of the flakes occurring upon the elimination of the functional groups. The central part of the flakes remains extremely flat contrary to what occurs with thermal reduction. These structural defects induced by chemical and thermal reduction processes are very probably the most important limitations for electrical conductivity in GO based electrodes. (C) 2014 Elsevier Ltd. All rights reserved.