<p>The impact of soil-structure interaction (SSI) should be considered in seismic fragility analysis of buildings on soft soils. Past SSI-related analyses focus on seismic fragility of buildings without integrating foundation damage probability into an SSI system level fragility. However, significant foundation damage may result in failure of an SSI system, even if the supporting superstructure remains elastic. Therefore, when performing seismic fragility analyses of buildings on soft soils, respective damage to the building and foundation should be quantified probabilistically so that an SSI system level seismic fragility function could be derived. To this end, this study proposes the use of a multivariable probabilistic seismic demand model (MPSDM) to account for correlations of seismic damage to various structural and foundation components. Combining the MPSDM with two alternative damage evaluation models, including a building-foundation-in-series model and a system-level damage state matrices (DSM) model, two seismic fragility analysis procedures for building-foundation systems are developed, respectively named as series-based and DSM-based methods. Results of a generic building-foundation system show that the system-level fragility curves are significantly higher than those at component levels. In fact, the system-level fragility may depend on various damage modes, associated with either excessive foundation rocking or substantial (residual) deformation of the superstructure. It is concluded that combined effects of multiple damage modes of components must be considered in seismic capacity to avoid underestimating the probability of severe damage of the whole system due to ignoring the combined effects of the damage modes for damage evaluation.</p>