Introduction of biofuels to the fuel matrix poses new questions and challenges. The present study investigates the microbiological stability of biodiesel blends in small scale microcosms. The study presents results from incubations of diesel-biodiesel blends with contaminated inoculation water collected from diesel storage tanks to ensure the presence of relevant fuel degrading bacteria. DAPI and qPCR analyses has subsequently shown an increased bacterial growth and activity in the microcosms containing biodiesel blends as the carbon source compared to those microcosms where neat fossil diesel made up the carbon source. Several anaerobic microorganisms have been identified after incubation. Presence of methanogens, sulfate-reducing bacteria and nitrate reducing bacteria has furthermore been confirmed by chemical analyses, supplemented by observations of methane formation in biodiesel incubations. The findings will contribute to the knowledge base for a safer introduction of biodiesel in the fuel matrix by employment of proper house-keeping and monitoring methods. (C) 2011 Elsevier Ltd. All rights reserved.