The purpose of this paper is to present the Soil-Tunnel-Structure Interaction analysis performed for the “innovative” seismic retrofit of the Posey and Webster Street Tunnels located in the San Francisco Bay area. The tunnels are situated between two major faults, the Hayward Fault and the San Andreas Fault (Figure 1). Due to its close proximity to the site, the Hayward Fault is the controlling fault for the Safety Evaluation Earthquake (SEE) event. The Hayward Fault is capable of generating a peak horizontal rock acceleration of 0.76g, and horizontal ground accelerations in excess of 0.5g. The duration of the seismic event may exceed 45 seconds. The high peak rock acceleration of the design earthquake, and the long duration of the event, will allow the build-up of pore pressures. This could lead to extensive liquefaction with the consequent flotation of the tunnels resulting in a structural failure. The 1989 Loma Prieta earthquake (estimated horizontal ground acceleration of about 0.2g at the site) was the most recent major seismic event that occurred near the Posy and Webster Street Tunnels. The Post Earthquake Investigation report indicated evidence of liquefaction on the Island of Alameda and in the vicinity of the tunnels. Consequently, in 1997 ground improvement and retrofit of a number of structural components of tunnel segments became part of the retrofit plan for the tunnels. The ground improvement will prevent flotation of the tunnels, and the retrofit of structural components will prevent major damage to the tunnels themselves. Located at each end of the tunnel is a portal structure. It was necessary to design an opening between the portal structures and tunnels to reduce the tunnel-portal interaction. The retrofit strategy for the structural components is to provide flexibility and significantly reduce the forces in the tunnel segments. Response-spectrum-compatible rock motion time histories were developed along the tunnel alignment. The rock motions were propagated towards the surface to obtain the ground motion at the centerline of the tunnels for the Soil-Tunnel-Structure Interaction analysis. The objectives of the analysis were to estimate the responses of the as-built and retrofit configurations of the tunnels due to seismic excitations. In addition the global model racking analyses complements the global model.