If seismic isolation system consists of elastic-damping bearings, it transforms protected object into the flow-frequency system. Thus, damping in SIS should be high enough to eliminate resonance effect. Therefore application of damping makes a problem of its parameters optimization relevant. Optimization criteria for damping parameters of seismic isolation systems within the stochastic problem definition have been stated in the article. Search methods of optimal parameters for various tasks descriptions (target functions) have been developed. Both synthesized accelerograms and real accelerograms of earthquakes have been used as external actions. Both linear and nonlinear damping model including seismic isolation system have been taken into consideration. Search algorithms of optimal parameters have been worked out in different cases. Proceeded analysis results can be applied to design damping in seismic isolation systems.