This study presents the development and application of a systematic model-based framework for bioprocess optimization. The framework relies on the identification of sources of uncertainties via global sensitivity analysis, followed by the quantification of their impact on performance evaluation metrics via uncertainty analysis. Finally, stochastic programming is applied to drive the process development efforts forward subject to these uncertainties. The framework is evaluated on four different process configurations for cellulosic ethanol production including simultaneous saccharification and co-fermentation and separate hydrolysis and co-fermentation (SSCF and SHCF, respectively) technologies in different operation modes (continuous and continuous with recycle). The results showed that parameters related to pretreatment (e.g. activation energy of the reaction for glucose production, order of the reaction. etc.), hydrolysis (inhibition constant for xylose on conversion of cellulose and cellobiose, etc.) and co-fermentation (ethanol yield on xylose, inhibition constant on microbial growth, etc.), are the most significant sources of uncertainties affecting the unit production cost of ethanol with a standard deviation of up to 0.13 USD/gal-ethanol. Further stochastic optimization demonstrated the options for further reduction of the production costs with different processing configurations, reaching a reduction of up to 28% in the production cost in the SHCF configuration compared to the base case operation. Further, the framework evaluated here for uncertainties in the technical domain, can also be used to evaluate the impact of market uncertainties (feedstock prices, selling price of ethanol, etc.) and political uncertainties (such as subsidies) on the economic feasibility of lignocellulosic ethanol production. (c) 2011 Elsevier Ltd. All rights reserved.