We report on the effect of the substrate on the vertical phase separation in spin-coated thin films of poly [(9,9-dioctylfluorenyl-2,7-diyl)-co-5,5-4',7'-di-2-thienyl-2',1',3'-benz othiadiazole] (APFO-3) blended with [6,6]-phenyl-C-61-butyric acid methyl ester (PCBM). Compositional depth profiles of the films are measured by dynamic secondary ion mass spectrometry (SIMS). We found that changing the substrate from silicon to gold affects the composition profile near the substrate interface. This is caused by a specific interaction between the polymer (APFO-3) and the gold surface, as confirmed by X-ray photoelectron spectroscopy (XPS). The composition profile in the area away from the substrate interface, as well as the enrichment of the free surface with APFO-3, remain however unaffected by the choice of substrate. The vertical composition was also analysed for APFO-3:PCBM films spin-coated on indium tin oxide (ITO) coated with a thin layer of (3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS). (c) 2006 Elsevier B.V. All rights reserved.