In this study, a thermoeconomic assessment of an integrated ethanol production from sugarcane bagasse and traditional sugarcane juice is developed and discussed. An integrated distillery, which works with first and second generation ethanol production routes, is modeled and simulated. The thermoeconomic model assumes that the only agricultural input to the processes is the sugarcane itself (straw or other wastes recovered from the field were not considered in the analysis). The analyses are carried out for three operating scenarios: scenario I describes a traditional distillery or a first generation distillery; scenario II takes into account an integrated distillery operating with current acid hydrolysis technology; scenario III describes an improved distillery which operates with future technology for hydrolysis and pentose fermentation. Exergy analysis, production cost analysis and economic viability assessment are carried out for each scenario. As a result, it can be concluded that the global exergy efficiency decreases with the bagasse hydrolysis for scenario II. This situation is reversed when pentose fermentation is considered in scenario III. The economic viability assessment shows that hydrolysis is not viable in the present Brazilian economic scenario because it causes a drop of 4.0% in the internal rate of return (IRR) for scenario II and 2.3% for scenario III, when compared to scenario I.