The nanoscale morphology of the active layer in organic, bulk heterojunction (BHJ) solar cells is crucial to device performance. Often a combination of casting conditions and post deposition thermal treatment is used to optimize the morphology. In general, the development of microscopic crystals is deleterious, as the exciton diffusion length is approximate to 10 nm. We find that the microscopic crystallization behavior in polythiophene/fullerene blends is strongly influenced by the substrate on which the BHJ is cast. With a silicon oxide substrate, the crystal nucleation density is high and significant crystallization occurs at a temperature of 140 degrees C. On more hydrophobic substrates, significantly higher temperatures are required for observable crystallization. This difference is attributed to the interfacial segregation of the PCBM, controlled by the substrate surface energy. The substrate dependence of crystallization has significant implications on the fullerene crystal growth mechanisms and practical implications for device studies. (C) 2011 Published by Elsevier B.V.