Dependence upon fossil sources and environmental concerns have been driving the research for alternative systems for automotive fuel production. In this work, a general modeling framework conceived to drive the decision-making process for the strategic design of biofuel supply networks is presented. The design task is formulated as a mixed integer linear program (MILP) that accounts for the simultaneous minimization of the supply chain operating costs (part 1) as well a the environmental impact in terms of greenhouse gas (GHG) emissions [part 2 (DOI 10.1021/ef9004779)], The model is devised for the integrated management of the key issues affecting a general biofuel supply chain, such as agricultural practice, biomass supplier allocation, production site locations and capacity assignment, logistics distribution, and transport system optimization. A spatially explicit approach has been adopted to capture the strong geographical dependence of the biomass cultivation practice performance. A purpose-designed financial model has also been embodied to consider the scale factors affecting the plant capacity assignment. In part 1, the proposed tool has been applied to design the emerging Italian corn-based ethanol system by optimizing economic criteria. The reported results demonstrate the framework capabilities to provide valuable insight in steering the design of strategic infrastructures.