The use of disodium peroxodisulphate combined with a neutral buffer is a new method for the efficient removal of organic matter from clay-bearing sediments. The effects of this oxidation procedure on mineral structure were investigated by treatment of different standard clay minerals (kaolinite ‘china clay’, illite ‘Le Puy’, montmorillonite SWy-1). The materials were characterized by means of XRD, FTIR, SEM and TEM before and after leaching with disodium peroxodisulphate. Systematic experiments were conducted to determine the effects of leaching on the chemical and isotopic composition of oxygen, hydrogen and K-Ar in these samples. Effects on the physicochemical properties of the clays such as BET external surface area, cation exchange capacity (CEC) and expandability with ethylene glycol were also investigated. The results show that structure, chemical composition, oxygen and hydrogen isotope ratios, as well as the K-Ar system remain unaffected by leaching with disodium peroxodisulphate. The CEC and expandability remain unchanged, whereas changes in BET area can be attributed to mechanical dispersion by ultrasonic treatment.