CdSe nanocrystals (NCs) can be used as an electron acceptor in solar cells, employing organic ligands to passivate their surface and make them processable from solution. The nature and abundance of impurities present after NC ligand exchange from oleic acid to n-butylamine are identified. A further purification step using hexane as a selective solvent is described, which excludes NC aggregates from solution. The influence of NC aggregates on photovoltaic device performance is studied in a CdSe:poly[2-methoxy-5-(3′,7′-dimethyloctyloxy)-1,4-phenylene vinylene] (MDMO-PPV) bulk heterojunction solar cell. The exclusion of NC aggregates leads to a four-fold increase in device power conversion efficiency (PCE) in optimized devices. A superior blend morphology leading to improved charge generation and a better NC percolation network is identified as the main causes of this increased solar cell performance.