All refineries are characterized by mixed feedstocks and a range of products, but biorefineries in particular can involve a very diverse range of 'bio' related material (of variable quality) as a feedstock. The subsequent processing steps may involve heterogeneous catalysis, immobilized enzymes, homogeneous catalysts, soluble enzymes, fermentations or combinations thereof, alongside purification steps. This presents a particularly interesting process integration challenge since the optimal conditions for each process step will be considerably different to each other, there are large temperature gradients through the process and a significant amount of water is used. The basic question to address is thus which product to produce and which sequence of unit operations to apply to obtain the highest profit for the biorefinery. Use of a systematic methodology to analyze and improve processing routes for a specific biorefinery product is therefore a useful first step in the evaluation of the biorefinery product tree. In this paper, we will illustrate the use of a systematic methodology for design and analysis using bioethanol production as an example. More specifically, we will consider a well-known bioethanol production route, analyze it with respect to cost, operation and sustainability, and based on these, generate new alternatives with respect to waste reduction (water) and efficient downstream separation. (C) 2009 The Institution of Chemical Engineers. Published by Elsevier B.V All rights reserved.