Since modern synchrotrons with highly intense X-ray beams are in use to investigate organic materials, the stability of soft matter materials during beam exposure is a crucial issue. Grazing incidence X-ray diffraction and specular X-ray reflectivity measurements were performed on thin films of organic semiconducting materials, like poly(3-hexylthiophene) (P3HT), sexithiophene and pentacene. These films were irradiated with an average flux density between 1015 and 1016photons/(smm2) and evidenced a different stability in synchrotron X-ray radiation. The semi-crystalline P3HT showed a clear intensity decrease of the 100 Bragg peak and 020 Bragg peak compared to the rather stable diffraction features of the molecular crystals sexithiophene and pentacene. The difference in synchrotron X-ray radiation stability is explained by the interaction of the X-ray beam with the individual chemical components in the molecules as well as by the different crystallinities of the materials. Furthermore, the semi-crystalline P3HT film exhibited an increase of film thickness after irradiation and the surface roughness slightly decreased. To summarize, this study shows a strong influence of synchrotron X-ray radiation to specific organic thin films like e.g. P3HT, while others like pentacene and sexithiophene are observed as quite stable.