In a companion paper, an overview and problem definition was presented for ground motion selection on the basis of the conditional spectrum (CS), to perform risk-based assessments (which estimate the annual rate of exceeding a specified structural response amplitude) for a 20-story reinforced concrete frame structure. Here, the methodology is repeated for intensity-based assessments (which estimate structural response for ground motions with a specified intensity level) to determine the effect of conditioning period. Additionally, intensity-based and risk-based assessments are evaluated for two other possible target spectra, specifically the uniform hazard spectrum (UHS) and the conditional mean spectrum (CMS, without variability).It is demonstrated for the structure considered that the choice of conditioning period in the CS can substantially impact structural response estimates in an intensity-based assessment. When used for intensity-based assessments, the UHS typically results in equal or higher median estimates of structural response than the CS; the CMS results in similar median estimates of structural response compared with the CS but exhibits lower dispersion because of the omission of variability. The choice of target spectrum is then evaluated for risk-based assessments, showing that the UHS results in overestimation of structural response hazard, whereas the CMS results in underestimation. Additional analyses are completed for other structures to confirm the generality of the conclusions here. These findings have potentially important implications both for the intensity-based seismic assessments using the CS in future building codes and the risk-based seismic assessments typically used in performance-based earthquake engineering applications. Copyright © 2013 John Wiley & Sons, Ltd.