This paper describes a series of seismic fragility analyses of base-isolated structures considering non-linear superstructure behavior. The Latin hypercube sampling technique is applied to construct a series of samples that explicitly account for non-Linear behavior. Fragility curves are generated that evaluate the limit state based on maximum superstructure ductility ratio. The study shows that base-isolation systems have a significant advantage for seismic protection compared with fixed-base structures. However, careful consideration should be given to the fact that plastic deformation demands on the superstructure can increase dramatically after yielding if the super-structure is designed anticipating a reduced seismic lateral shear force.