Bio-fuels represent promising candidates for renewable liquid fuels. One of the challenges for the emerging industry is the high level of uncertainty in supply amounts, market demands, market prices, and processing technologies. These uncertainties complicate the assessment of investment decisions. This paper presents a model for the optimal design of biomass supply chain networks under uncertainty. The uncertainties manifest themselves as a large number of stochastic model parameters that could impact the overall profitability and design. The supply chain network we study covers the Southeastern region of the United States and includes biomass supply locations and amounts, candidate sites and capacities for two kinds of fuel conversion processing, and the logistics of transportation from the locations of forestry resources to the conversion sites and then to the final markets. To reduce the design problem to a manageable size the impact of each uncertain parameter on the objective function is computed for each end of the parameter's range. The parameters that cause the most change in the profit over their range are then combined into scenarios that are used to find a design through a two stage mixed integer stochastic program. The first stage decisions are the capital investment decisions including the size and location of the processing plants. The second stage recourse decisions are the biomass and product flows in each scenario. The objective is the maximization of the expected profit over the different scenarios. The robustness and global sensitivity analysis of the nominal design (for a single nominal scenario) vs. the robust design (for multiple scenarios) are analyzed using Monte Carlo simulation over the hypercube formed from the parameter ranges. (C) 2011 Elsevier Ltd. All rights reserved.