The influence of fullerene side chain functionalization on both the morphology and electro-optical properties of bulk-heterojunction polymer:fullerene solar cells is discussed through a systematic investigation of material blends consisting of the conjugated polymer poly[2-methoxy-5-(3′,7′-dimethyloctyloxy)-1,4-phenylene vinylene] (MDMO-PPV) as donor and fullerene molecules with different side chains as the acceptor. The varying side chain of the fullerenes was found to induce morphological changes as confirmed by different analytical techniques such as Transmission Electron Microscopy (TEM), X-ray Diffraction (XRD), and Nuclear Magnetic Resonance (NMR). The fullerene with the shorter side chain, [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), forms crystalline nanophases in the blend, while this is not the case for the alternative diphenylmethanofullerene acceptor, [6,6]-1,1-bis(4,4′-dodecyloxyphenyl)methanofullerene (DPM-12). The introduction of NMR allows us to estimate the fraction of crystalline fullerene. The morphological changes have a profound effect on the characteristics of charge transfer states (CT) formed at the polymer:fullerene interfaces. Crystallization of fullerene molecules shifts the energy of the CT state. This shift in energy is directly manifested in the open-circuit voltage of solar cells based on the fullerene acceptors under investigation.