Two immersed tube tunnels used for vehicular traffic in the seismically active San Francisco Bay Area were built over 30 years ago with little consideration to seismic effects. A seismic retrofit study was conducted to assess the vulnerability of the tubes to seismic shaking and to develop necessary retrofit schemes. Three-dimensional soil-structure interaction models of the tunnels and portal buildings were developed to simulate the structures response to earthquake induced ground motions. The analyses showed that the existing continuous joints that connect the tube segments would result in the transmittal of significant axial forces and moments, which can cause cracking in the tubes, and damage to the portal buildings. A retrofit design was developed where the immersed tube segment joints were released in tension and gaps were provided at the tube-portal building joints. Analyses of the proposed retrofit scheme showed a reduction of forces and displacements to acceptable levels.