Extended Activated sludge model 3 (ASM3), with the incorporation of soluble microbial products (SMP) concept and simultaneous growth and storage phenomenon, was a useful tool for investigating the biological process in membrane bioreactors (MBRs). Estimating and evaluating the sensitivity and uncertainty associated with the model simulation was a critical task for exhibiting the reliability and transparency of the results. On the basis of extended Fourier amplitude sensitivity test (extended FAST), this study quantified the uncertainty involved in predicting the biological process at different sludge retention times (SRTs = 10, 30 and 50 day), including sludge production, organic removal. SMP production and nitrification efficiency. It was found that the interpretation of sensitivity analysis results depended much on the operated SRT, hence the framing of the analysis. The importance ranking quantified the parameters' main effects on model outputs and explained the sum of the effects, thus permitting informed decisions for uncertainty reduction. (C) 2011 Elsevier B.V. All rights reserved.