Abstract Biofuels from bioenergy crops may substitute a significant part of fossil fuels in the transport sector where, e.g., the European Union has set a target of using 10% renewable energy by 2020. Savings of greenhouse gas emissions by biofuels vary according to cropping systems and are influenced by such regional factors as soil conditions, climate and input of agrochemicals. Here we analysed at a regional scale the greenhouse gas (GHG) emissions associated with cultivation of winter wheat for bioethanol and winter rapeseed for rapeseed methyl ester (RME) under Danish conditions. Emitted CO2 equivalents (CO2eq) were quantified from the footprints of CO2, CH4 and N2O associated with cultivation and the emissions were allocated between biofuel energy and co-products. Greenhouse gas emission at the national level (Denmark) was estimated to 22.1 g CO2eq MJ−1 ethanol for winter wheat and 26.0 g CO2eq MJ−1 RME for winter rapeseed. Results at the regional level (level 2 according to the Nomenclature of Terr...