Biofuels are likely to play an increasingly important role in the transportation sector in the coming decades. To ensure the sustainability of the biofuel chain, regulatory criteria and reduction targets for greenhouse gases (GHG) emissions have been defined in different legislative frameworks (e.g. the European Renewable Energy Directive, RED). The provided calculation methods, however, leave room for interpretation regarding methodological choices, which could significantly affect the resulting emission factors. In this study, GHG reduction factors for a range of biofuels produced in a Danish biorefinery system were determined using five different emission allocation principles. The results show that emission savings ranged from -34 % to 71 %, indicating the need for a better definition of regulatory calculation principles. The calculated emission factors differed significantly from default values provided in the literature, suggesting that case-specific local conditions should be taken into consideration. A more holistic LCA-based approach proved useful in overcoming some of the issues inherent in the regulatory allocation principles. On this basis, indirect land use change (ILUC) emissions were shown to have the same magnitude as the direct emissions, thus indicating that the overall system should be included when assessing biofuel sustainability criteria.