The secondary metabolites accumulated in a pervaporation membrane bioreactor during ethanol fermentation were mostly composed of acetic acid, lactic acid, propionic acid, citric acid, succinic acid and glycerol. The inhibition effect of these compounds at a broad concentration range was studied through ethanol fermentation by Saccharomyces cerevisiae. An increasing concentration of the secondary metabolites led to longer lag time and a reduction of cell growth. The specific cell growth rate, cell yield, ethanol productivity were only 0.061 h(-1), 0.024, 0.47 g L-1 h(-1) respectively, when the medium contained 3.12 g of acetic acid, 10.23 g of lactic acid, 2.72 g of propionic acid, 1.35 g of citric acid, 2.26 g of succinic acid and 49.25 g of glycerol per liter (a concentration level in pervaporation membrane bioreactor at later fermentation period). By increasing pH of the medium to 6.0-8.0, the inhibition of these secondary metabolites could be greatly relieved. (C) 2014 Elsevier Ltd. All rights reserved.