This thesis explores how active layer morphology and opto-electronic properties change in different types of fullerene containing solar cells as a function of molecular structure. We studied the experimental variations in small molecule organic devices containing different donors from the diketopyrrolopyrrole family as well as devices containing different acceptors from the diphenylmethanofullerene class. We also generated a large database of molecular structures using experimental values in order to build statistical models for the prediction of electrical properties in this type of devices using 2D or DFT descriptors derived from donor molecule structures. Finally we also explored the opto-electronic properties of fullerene containing lead halide perovskite solar cells, implementing a new fabrication technique within our research group and creating a link between the photophysical behavior of lead halide perovskite and small molecule organic solar cells. This thesis takes an initial look into the very complex relationships between molecular structure and organic solar cell device performance, taking an approach that ultimately attempts to take us closer to the rational design of molecules that have the ideal properties to produce highly performing fullerene containing solar cells.