The purpose of this paper is to develop a model for the decision-makers/stakeholders to design biofuel supply chain under uncertainties. Life cycle energy and CO2 emission of biofuel supply chain are employed as the objective functions, multiple feedstocks, multiple transportation modes, multiple sites for building biofuel plants, multiple technologies for biofuel production, and multiple markets for biofuel distribution are considered, and the amount of feedstocks in agricultural system, transportation capacities, yields of crops, and market demands are considered as uncertainty variables in this study. A biobjective interval mix integer programming model has been developed for biofuel supply chain design under uncertainties, and the bio-objective interval programming method has been developed to solve this model. An illustrative case of a multiple-feedstock-bioethanol system has been studied by the proposed method, and the results show that the proposed model can help decision-makers/stakeholders plan and design the biofuel supply chain by proposing feasible solutions to them. (C) 2016 Elsevier Ltd. All rights reserved.