Owing to tremendous research efforts, the efficiency of organic small molecule solar cells has increased substantially over the past decade and has now surpassed the 10% efficiency limit. An important factor affecting the performance of such solar cells is the morphology of the n- and p-type domains in the active organic layer. The molecular packing in these is of same importance, as it strongly affects the carrier transport in the cells. In this work, we present the study of alpha-sexithiophene (α 6T) temperature dependent growth for standard, on gold anodes, and inverted, on electron accepting C60 layers, solar cell configurations. Furthermore, a comparative study of the correlation between the α-6T morphology and device performance parameters for standard and inverted solar cell configurations is presented. The morphology of the α 6T layer is controlled by means of the substrate temperature during low rate (<0.5Å/s) organic molecular beam deposition, which results in α-6T layers ranging from continuous films and dispersed clusters at low temperatures, to larger crystalline nanostructures at higher temperatures. Optical and atomic force microscopy is conducted together with crystallographic techniques in order to determine the morphology of the grown α 6T thin-films, as well as the molecular orientation within the electron donor.