Pretreatment of Estonian oil shale by thermophilic Sulfolobus acidocaldarius and mesophilic Thiobacillus ferrooxidans in order to remove inorganic sulphur compounds (pyrite) has been studied. Shake flask experiments showed bacterial growth on the internal pyrite of the shale and no substrate toxicity. The bioreactor experiments demonstrated that the oxidation of pyrite by S. acidocaldarius is especially fast (96 % in four days). However, to evaluate the economic feasibility of the process, the high acid consumption of this oil shale has to be taken into consideration.