Earthquakes subject tunnel linings to transient strains due to ground shaking, and can cause localized permanent strains in zones of fault rupture. These issues are discussed with respect to seismic analyses and design strategies. Most underground structures are flexible in relation to the ground, and these structures will be subject to the same strains as the ground in which they are embedded, yet such strains often do not drive structural design. However, without design detailing to create strain compatibility, large changes in structural flexibility can create undesirable changes in strain due to seismic shaking. Similarly, while it is impossible to design a tunnel lining to resist discrete fault movement, measures can be taken to minimize damage and facilitate repair following a major earthquake. Two case histories illustrate these concepts: (1) the Bay Tunnel in Santa Clara County, California, a new water supply tunnel in soft ground near active faults and subject to severe seismic shaking; and (2) the Claremont Tunnel Seismic Upgrade in Berkeley, California, retrofit of a water supply tunnel crossing an active fault.