Oil shales are one of the alternative sources of hydrocarbon fuels (“synthetic petroleum”), characterized by the increased sulfur and nitrogen content which represent even greater ecological problem in use, compared to classical fuels. Acidithiobacillus ferrooxidans is capable of oxidizing pyrite to iron (III)-ion, providing a strong oxidation agent at low pH. We have used this oxidizing agent for oxidation of sulfur present in DBT as a substrate model to demonstrate its potential to oxidize organically bound sulfur in oil shales. An HCl-concentrate was used as the hydrocarbon matrix. Acidithiobacillus ferrooxidans is already recognized to oxidize the pyritic sulfur component, thereby potentially providing a complete sulfur removal system. By applying GC-MS we established that DBT transformation occurred by oxidation or elimination of sulfur. The products obtained are more soluble in water than parent compounds and this reduces concentration of organic sulfur.