Biofuels are increasingly promoted worldwide as a means for reducing greenhouse gas (GHG) emissions from transport. However, current regulatory frameworks and most academic life cycle analyses adopt a deterministic approach in determining the GHG intensities of biofuels and thus ignore the inherent risk associated with biofuel production. This study aims to develop a transparent stochastic method for evaluating UK biofuels that determines both the magnitude and uncertainty of GHG intensity on the basis of current industry practices. Using wheat ethanol as a case study, we show that the GHG intensity could span a range of 40-110 gCO2e MJ-1 when land use change (LUC) emissions and various sources of uncertainty are taken into account, as compared with a regulatory default value of 44 gCO2e MJ-1. This suggests that the current deterministic regulatory framework underestimates wheat ethanol GHG intensity and thus may not be effective in evaluating transport fuels. Uncertainties in determining the GHG intensity of UK wheat ethanol include limitations of available data at a localized scale, and significant scientific uncertainty of parameters such as soil N2O and LUC emissions. Biofuel polices should be robust enough to incorporate the currently irreducible uncertainties and flexible enough to be readily revised when better science is available. © 2013 IOP Publishing Ltd.