A diapiric intrusion of clays in the Carlentini Formation (Tortonian) was discovered in a quarry at S. Demetrio High (Hyblean Plateau, Sicily, Italy). Seven clay samples were analyzed by different analytical methods, including X-ray powder diffraction (XRD) and Fourier-transform infrared (FTIR) spectroscopy, to determine the composition and mechanism of formation (sedimentary vs. hydrothermal) of these clays. Ferric saponite, carbonates (calcite and traces of ankerite), quartz, pyrite, and zeolites (phillipsite and harmotome) were detected using XRD and FTIR. This mineral assemblage, dominated by Fe-rich saponite, and the abundance of light rare-earth elements (LREE), Eu, fluid-mobile elements (FME > 10 × primordial mantle: Li, Be, B, As, Sb, Pb, U, Ba, Sr, Cs), and other incompatible elements (Zr = 169 ppm, Nb = 46 ppm, Th = 11 ppm, on average) imply that S. Demetrio clays precipitated from a mixture of hot Si-rich hydrothermal fluids (350–400°C) and cold seawater. The evidence is in accord with the affinity of clays for hydrothermally modified mafic and ultramafic rocks, forming the Hyblean lower crust, based on multi-element comparisons, and on the occurrence of trace amounts of chrysotile 2M_c1 and sepiolite. The association of long-chain aliphatic-aromatic hydrocarbons (intensity ratios I₂₉₂₇/I₂₉₅₇ > 0.5) with hydrothermal clays, the lack of fossils, and the similarity of the IR absorption bands with those of organic compounds detected previously in some metasomatized Hyblean gabbroic xenoliths suggest a possible abiogenic origin of hydrocarbons via a Fischer-Tropsch-type reaction. The S. Demetrio clay diapir was emplaced at shallow crustal levels in the Late Miocene as a consequence of the interaction, at a greater depth, of an uprising basalt magma and the products of an early, serpentinite-hosted hydrothermal system.