The last decade of performance-based earthquake engineering (PBEE) research has seen a rapidly increasing emphasis placed on the explicit quantification of uncertainties. This paper examines uncertainty consideration in input ground-motion and numerical seismic response analyses as part of PBEE, with particular attention given to the physical consistency and completeness of uncertainty consideration. It is argued that the use of the commonly adopted incremental dynamic analysis leads to a biased representation of the seismic intensity and that when considering the number of ground motions to be used in seismic response analyses, attention should be given to both reducing parameter estimation uncertainty and also limiting ground-motion selection bias. Research into uncertainties in system-specific numerical seismic response analysis models to date has been largely restricted to the consideration of ‘low-level’ constitutive model parameter uncertainties. However, ‘high-level’ constitutive model and model methodology uncertainties are likely significant and therefore represent a key research area in the coming years. It is also argued that the common omission of high-level seismic response analysis modelling uncertainties leads to a fallacy that ground-motion uncertainty is more significant than numerical modelling uncertainty. The author's opinion of the role of uncertainty analysis in PBEE is also presented. Copyright © 2013 John Wiley & Sons, Ltd.