Blends of the low-bandgap polymer poly [(9,9-dioctylfluorenyl-2,7-diyl)-co-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole] (APFO-3) and the fullerene derivative [6,6]-phenyl-C-61-butyric acid methyl ester (PCBM) were spin-coated from chloroform solution into thin films, which were examined with dynamic secondary ion mass spectrometry. For blends with high PCBM content, the depth profiles show composition waves that were caused by surface-directed phase separation during spin-coating. The formation of such multilayer structures by spontaneous self-stratification is likely to have implications for optimization strategies for the performance of organic solar cells.