Refining catalysis has been developing over many years to satisfy the demand for high-quality and environmentally-acceptable automotive fuels. Biomass-derived feedstocks have been recently introduced into refineries posing thus new challenges for refining processes and catalysis. The manuscript focuses on three prominent biomass-derived feedstocks: triglycerides, bio-oils and Fischer-Tropsch products from gasified biomass. Due to high oxygen content in biomass feedstocks, deoxygenation processes play an important role in upgrading of these feedstocks. Thus, first peculiarities of deoxygenation are discussed in detail in the context of hydrotreatment processes. Different possibilities of triglycerides and bio-oils deoxygenation including their coprocessing with crude-oil-derived fractions are described. Since biomass-to-liquid processes are very important for the conversion of general biomass into liquid products, the second part deals with the aspects of biomass conversion to synthesis gas, Fischer-Tropsch synthesis and introduction of new co-catalysts.