In a molecular photovoltaic device, charge separation and energy conversion result from the evolution of a photogenerated exciton into a charge separated state, in competition with recombination to ground. The efficiency of charge separation is a function of the molecular packing and energy level alignment near the interface, and of disorder in these properties. Understanding the effect of structure, energetics and disorder on the competition between charge separation and recombination helps to identify the factors controlling device photovoltage and ultimately conversion efficiency. Here, we address the factors controlling generation efficiency and photovoltage in molecular donor: acceptor solar cells using a combination of electrical and spectroscopic measurements and numerical models. We explore the limits to Voc using a model of non-radiative recombination, and demonstrate how choice of materials and control of processing may influence voltage losses. We use these results to consider the importance of chemical structure, the phase behaviour and microstructure of the binary system in controlling actual performance and the ultimate limitations placed on solar to electric conversion by the molecular nature of the materials. We also address methods for the experimental determination of non-radiative recombination rates.