The rare earth element (REE) content of the Tunisian Permian–Neogene shales have been studied to determine the origins of the clay minerals in these shales. The Permian–Neogene series overlies the Palaeozoic basement that has been studied via oil-drilling cores. This study of REEs was performed in various palaeogeographical domains of Tunisia, from the ‘Saharan Platform’ in the south to the ‘Nappes Zone’ in the north. In this work, those levels rich in illite (Palaeozoic, Triassic and Jurassic), smectite (Campanian–Maastrichtian) and palygorskite (continental Eocene) as well as some Miocene levels rich in halloysite are examined. The distribution of REEs in the Tunisian margin sediments is generally homogeneous, except for the Miocene levels containing halloysites. The normalization curves of REEs vs North American shale composite characterize the inherited clays regardless of the dominant minerals, except for a few cases of neoformation. The flat REE curves indicate a detrital origin of the studied clay levels.