The search for alternatives to conventional fuels becomes more and more important. Second generation biofuels might be a solution to provide us with renewable energy. There are several alternatives to the fossil fuels, such as ethanol, isobutanol, sesquiterpenoids and fatty acid ethyl esters (FAEEs). Saccharomyces cerevisiae is a potent and versatile cell factory, which is able to produce these substances. Except for ethanol the so far achieved yields need to be improved. S. cerevisiae has to be equipped with the proper tools to degrade lignocellulose. This can be achieved by different strategies: secretion or cell surface display of lignocellulose-degrading enzymes, synthesis of cellulosomes or intracellular cellodextrin hydrolysis. Many filamentous fungi possess the ability to efficiently degrade lignocellulose, but they do not produce larger quantities of ethanol due to intolerance towards the product and anaerobic conditions. Therefore, the goal of production of second generation biofuels could also be achieved by enabling them to produce and tolerate higher amounts of ethanol.