A performance based approach for site response analysis requires a probabilistic approach accounting for the observed variability in soil stratification and engineering properties of the soil layers. The major variability in site-specific response analysis arises from the uncertainties induced by the (a) local seismic hazard assessment, (b) selection and scaling of the hazard compatible input earthquake time histories, (c) soil stratification and engineering properties of encountered soil and rock layers, and (d) method of site response analysis. Even though the uncertainties related to first item, local seismic hazard assessment, has primary importance on the outcome of the site-specific response analyses, the discussion in this article focuses on the possible uncertainties in selection and scaling of the hazard compatible input earthquake time histories, soil stratification, thickness, type and their engineering properties, depth of ground water table and bedrock and properties of the engineering bedrock. One alternative may be to conduct site response analyses for large number of soil profiles generated by Monte Carlo simulations using relatively large number of hazard compatible acceleration time histories to assess probabilistic performance based design acceleration spectra and acceleration time histories calculated on the ground surface with respect to different performance levels. A remaining issue may be considered as the variability induced by 1D, 2D, and 3D site response analysis.