A range of economic and societal issues has resulted from fossil fuel consumption in the transportation sector in the U.S. These include health related air pollution, climate change, dependence on imported oil, and other oil related national security concerns. Biofuels production from various lignocellulosic biomass types, such as wood, forest residues, and agriculture residues, have the potential to replace a portion of the total fossil fuel consumption. This study focused on locating biofuel facilities and designing the biofuel supply chain to minimise the overall cost. For this purpose, an integrated methodology was proposed by combining the Geographic Information System technology with simulation and optimisation modelling methods. The GIS-based method was used as a precursor for selecting biofuel facility locations by employing a series of decision factors. The identified candidate sites for biofuel production served as inputs for simulation and optimisation modelling. The simulation/optimisation model and identified locations provided an integrated decision support system for decision makers to determine the optimal cost, energy consumption, and emissions for candidate locations. This novel methodology development extends prior research. (C) 2015 Elsevier Ltd. All rights reserved.