3,4,9,10-perylene tetracarboxylic diimide molecules were evaporated onto a Sn/ Si(111)-23×23 surface and studied using photoelectron spectroscopy and near edge X-ray absorption fine structure (NEXAFS). We found evidences of a strong interaction between the PTCDI molecules and the substrate. The interactions cause changes in the Sn 4d, C 1s, and N 1s core level spectra. These interactions also cause a complete absence of transitions to the lowest unoccupied molecular orbital (LUMO) in the NEXAFS spectra, in combination with a new state between the regular highest occupied molecular orbital (HOMO) and the Fermi level at low coverages. These changes are explained to be due to the charge transfer from the top Sn atoms to the PTCDI molecules, resulting in a split of the HOMO, and lowering of the LUMO levels. The interactions are shown to heavily involve the carbonyl carbon and partly nitrogen atoms of the imide group.