Novel fullerene derivatives bearing thiophene and furan residues were synthesized and studied as electron acceptor materials in bulk heterojunction organic solar cells, together with poly(3-hexylthiophene) (P3HT) as the donor polymer. Some compounds showed large nanomorphological inhomogenities in blends with P3HT; in particular, clusters with dimensions in the range of 100–1000 nm were formed. However, some blends that showed such large clusters yielded at the same time high power conversion efficiencies in photovoltaic devices, approaching 3.7 %. This is in sharp contrast with previously studied systems, in which a substantial phase separation always resulted in a poor photovoltaic performance. We assume that the attachment of thienyl or furyl groups to the fullerene cage results in a certain ordering of the designed fullerene derivatives I–IX with P3HT in photoactive blends. Both the fullerene derivative and P3HT might assemble via π–π stacking of the thiophene units to form the nanostructures observed in the films by optical and atomic force microscopy. The presence of ordered donor and acceptor counterparts in these nanostructures results in superior photovoltaic device operation.