In a linear-elastic dynamic analysis approach often the effect of some characteristics which could have significant impact on the seismic response of a bridge are missed. This is because such effects are either simply ignored or cannot be easily and realistically modeled. These include: (1) intermediate expansion joints with: (a) sliding bearings, (b) gapped-yielding earthquake restrainers with tension-only properties, (c) joint closure with impacting; (2) formation and deformation of plastic hinges and redistribution of forces; (3) soil-structure interaction with nonlinear soils; (4) large displacement effects; (5) buckling and post-buckling behavior; (6) isolation; (7) damping. Nonlinear dynamic analysis of long-span bridges can be used to more accurately and realistically predict their seismic response than elastic dynamic response, and used for more cost effectively upgrading the seismic resistance of existing long-span bridges. Seismic response analysis of long-span bridges for design or retrofitting can be performed using a combination of static nonlinear analysis and dynamic nonlinear time-history analysis. Nonlinear analysis techniques are generally available to the practicing bridge engineers, however the results obtained must be thoroughly examined and used with caution. This paper discusses the application of nonlinear analysis techniques used in the seismic upgrading of the Golden Gate Bridge, Benicia-Martinez Bridge, and the Hernando DeSoto, I-40 Bridge across the Mississippi River. Selected modeling strategies used for the three bridges mentioned above are presented. Additionally, the results obtained for the local and overall response and the rationale used in determining vulnerable components and their retrofit will be discussed.