The purpose of this paper is to develop a model for designing the most sustainable bioethanol supply chain. Taking into consideration of the possibility of multiple-feedstock, multiple transportation modes, multiple alternative technologies, multiple transport patterns and multiple waste disposal manners in bioethanol systems, this study developed a model for designing the most sustainable bioethanol supply chain by minimizing the total ecological footprint under some prerequisite constraints including satisfying the goal of the stakeholders', the limitation of resources and energy, the capacity of warehouses, the market demand and some technological constraints. And an illustrative case of multiple-feedstock bioethanol system has been studied by the proposed method, and a global best solution by which the total ecological footprint is the minimal has been obtained. (C) 2013 Elsevier Ltd. All rights reserved.