The second largest cost in fuel ethanol production is from energy consumption with ethanol distillation and stillage treatment, particularly when stillage is treated by the multi-evaporation process. Therefore, stillage backset is the most economically competitive strategy for reducing discharge and saving energy consumption. In this article, continuous ethanol fermentation was performed by the flocculating yeast under stillage backset conditions. Compared to regular yeast, immobilized yeast within the fermentor through flocculation reduced byproducts formation in the stillage, since heat lysis of yeast during ethanol distillation was prevented, and many side reactions were thus eliminated, making more stillage backset within the fermentation system possible. Although pyruvic acid, succinic acid, citric acid, a-ketoglutaric acid, fumaric acid and glycerol from yeast metabolism, furfural and 5-hydroxymethyl furfural from process operations, and acetic acid and lactic acid from slight contamination were accumulated with the stillage backset, they had no significant impact on yeast growth and ethanol fermentation due to low concentrations accumulated within the fermentation system. However, propionic acid that was generated mainly during hydrolysate sterilization and distillation of the fermentation broth was detected as the major inhibitor, but this byproduct would be significantly reduced under industrial conditions without hydrolysate sterilization, making the stillage backset more reliable for industrial application. (C) 2013 Elsevier Ltd. All rights reserved.