The microstructures of chemical bath deposited CdS and electrodeposited CdTe polycrystalline thin films, in n-CdS/p-CdTe solar cells, were studied. In both CdS and CdTe, the effect of grain size, re-crystallisation and interdiffusion are linked to the tin oxide/glass substrate and deposition control. Optical characterisation and device measurements are used to qualify these changes in the context of solar cell fabrication.