The potential application of biochemical catalysis in the petroleum refining industry is discussed by a prospective analysis of the available data on the microbial and enzymatic modification of oil products. The proposed biotechnological processes can be considered either alternative or complementary to conventional oil refining technologies. Desulfurization, denitrogenation, asphaltene upgrading, heavy metal removal, and effluent treatment by enzyme-mediated reactions are reviewed. The introduction of novel nonconventional techniques in the petroleum industry may improve its energetic efficiency and reduce its environmental impact.