Seismic isolation is often used in protecting mission-critical structures including hospitals, data centers, telecommunication buildings, etc. Such structures typically house vibration-sensitive equipment which has to provide continued service but may fail in case sustained accelerations during earthquakes exceed threshold limit values. Thus, peak floor acceleration is one of the two main parameters that control the design of such structures while the other one is peak base displacement since the overall safety of the structure depends on the safety of the isolation system. And in case peak base displacement exceeds the design base displacement during an earthquake, rupture and/or buckling of isolators as well as bumping against stops around the seismic gap may occur. Therefore, obtaining accurate peak floor accelerations and peak base displacement is vital. However, although nominal design values for isolation system and superstructure parameters are calculated in order to meet target peak design base displacement and peak floor accelerations, their actual values may potentially deviate from these nominal design values. In this study, the sensitivity of the seismic performance of structures equipped with linear and nonlinear seismic isolation systems to the aforementioned potential deviations is assessed in the context of a benchmark shear building under different earthquake records with near-fault and far-fault characteristics. The results put forth the degree of sensitivity of peak top floor acceleration and peak base displacement to superstructure parameters including mass, stiffness, and damping and isolation system parameters including stiffness, damping, yield strength, yield displacement, and post-yield to pre-yield stiffness ratio.