Structural properties of a single crystal and of a thin film of 3,4,9, 10-perylene-tetracarboxylic-acid-diimide are compared. The two samples are both obtained from the vapour phase, the latter being deposited at room temperature, in an ultrahigh vacuum environment, on a clean Pt(100) substrate. In the single crystal we have pointed out interactions between adjacent molecules by overlapping of the pi systems in the stacks and by hydrogen bonds between neighbouring stacks. The various surface unit cells of the nanocrystals from the film, identified by means of scanning tunnelling microscopy, are not comparable to those expected from the X-ray diffraction study of the single crystal and to those already published for other substrates. This fact clearly highlights the role played by the type of substrate chosen and/or the substrate-molecule interaction that affects the stacking and crystallinity of the growing crystal on top. (c) 2006 Elsevier B.V All rights reserved.