The diagenetic evolution of clay minerals in a 4249 m sedimentary-magmatic sequence of the Zemah-1 drillhole in the Dead Sea Rift, Israel, was studied, mainly by X-ray diffraction (XRD). The parallel maturation of the organic matter was estimated by the thermal alteration index (TAI) method. Both parameters follow a progressive diagenesis with depth. The original clays, now encountered only at shallow depths, were dioctahedral, and mostly detrital. They transformed into Mg-rich trioctahedral clays starting with a saponite-dominated assemblage, followed by a saponite, ordered chlorite-smectite (C-S), and chlorite assemblage, and finally by a saponite, corrensite, chlorite and talc assemblage. Significant mineralogical composition gaps occur between saponite to corrensite and corrensite to chlorite. Short-range variations within the most evolved assemblage are controlled by bulk-rock composition. Depths of first occurrence and disappearance of minerals indicate a much higher geothermal gradient in the past whereas the TAI values suggest an even higher palaeogradient of ~70°C km−1.