In this study, we test if cost-efficient X-ray fluorescence (XRF) analyses can be used to fingerprint Palaeogene clay and marl deposits in Denmark. A total of 67 samples from key sites in Denmark have been analysed. Our preliminary results indicate that it is possible locally within 10–30 km to distinguish between most of the Palaeogene units, but on a regional scale across Denmark, the units are not unique, and this probably reflects variations in clay mineralogy, grain size and calcareous content. Accordingly, we suggest that a comprehensive reference database is now needed if the full potential of the method is to be utilised, and this will ultimately result in more reliable geological models.