The organic photovoltaic technology has developed much in the last few years thanks to the optimization of the solar cell geometry and, specially, to the research for new performing materials. Nevertheless, much work has still to be done in order to better know the real mechanisms regulating the function of such novel class of semiconductors. The study of thin-film micro-structure, and the influence of the deposition parameters on it, is an important issue in order to obtain best optical and electrical properties. Thermal evaporation in high-vacuum chambers is the more suitable deposition technique to obtain organic thin-films with well organize molecular structure. Deposition parameters such as the substrate temperature and deposition rate may have some important effect on the molecules ordering. In this paper the effects of substrate temperature on structural and optical properties have been studied for N,N′-ditridecyl perylene diimide (PTCDI-C13) thin-films. Four samples have been deposited at 30, 60, 90 and 120°C substrate temperature and their absorption has been investigated by photothermal deflection spectroscopy (PDS) and transmittance spectroscopy. Moreover, simulations of the transmittance spectra have been calculated in order to obtain the optical constants n and k. Finally atomic force microscopy (AFM) has been employed to analyze the superficial morphology of the thin-films.