The adsorption of perylene on the Si(001) surface is studied by means of first-principles density-functional theory calculations. Our results indicate that perylene adsorbs in an upright way in accordance with experimental observations. A number of conceivable geometries are considered and compared with respect to their adsorption energies, to their behavior in scanning tunnelling microscopy experiments and to their spectral response in an electron energy loss setup. Only the combination of these three aspects allows for the unique identification of the realized adsorption structure. In order to obtain complete energy loss spectra that can be related directly to experiments a recently developed method is used which allows for the easy calculation of both vibrational frequencies and intensities.