Biofuels are forms of energy (heat, power, transport fuels or chemicals) based on different kinds of biomass. There is much discussion on the availability of different biomass sources for bioenergy application and on the reduction of greenhouse gas emissions compared to conventional fossil fuels. There is much less discussion on the other effects of biomass such as the acceleration of the nitrogen cycle through increased fertilizer use resulting in losses to the environment and additional emissions of oxidized nitrogen. This paper provides an overview of the state of knowledge on nitrogen and biofuels. Increasing biofuel production touch upon several sustainability issues for which reason sustainability criteria are being developed for biomass use. We propose that these criteria should include the disturbance of the nitrogen cycle for biomass options that require additional fertilizer inputs. Optimization of the nitrogen use efficiency and the development of second generation technologies will help fulfill the sustainability criteria. © 2009 Springer Science+Business Media B.V.