This dissertation approaches the subject of three-dimensional (3D) seismic analysis of reinforced concrete (RC) wall buildings at near-fault sites by first studying two main problems separately: (1) the characterization of base excitation for buildings located at near-fault sites, and (2) modeling the behavior of RC buildings accurately including inelastic behavior and the failure mode. The dissertation culminates with the 3D response history analysis of two 20-story RC core wall buildings models, including the slabs and columns, subject to a strong near-fault ground motion record. First, the presence and characteristics of multiple pulses [with dominant period TP between 0.5 and 12 s] in historical near-fault ground motion records is studied. An iterative method for extracting multiple strong pulses imbedded in a ground motion is presented. The method is used to extract multiple strong velocity pulses from the fault-normal horizontal component of 40 pulse-like ground motion records from 17 historical earthquakes, with magnitudes ranging from MW6.3 to MW7.9, recorded at a distance less than 10 km from the fault rupture with a peak ground velocity greater than 0.6 m / s. The relationships between the dominant period of the extracted pulses, associated amplitudes, and earthquake magnitude are presented, indicating that the amplitude of the strongest pulses with 1.5 s ≤ TP ≤ 5 s, does not depend significantly on the earthquake magnitude. Next, the effect of soil-foundation-structure interaction (SFSI) for a 20-story core wall building with a caisson foundation subject to single pulse motions is investigated using two-dimensional (2D) nonlinear finite-elements and fiber beam-column elements; nonlinear site effects on the free-field motion and structural response is discussed. The nonlinear site effects for free-field motions result in a de-amplification of peak surface acceleration due to soil yielding, and a maximum of 64% amplification of peak acceleration and velocity of at specific pulse periods for deep soils. SFSI, after removing the nonlinear site effect, has a negligible effect on the maximum value of peak roof acceleration and peak roof drift ratio over the pulse periods considered; however, the effect of the increased flexibility due to SFSI is observed in the peak drift ratio and peak base shear response. A couple of chapters of this dissertation are dedicated to the development and verification of a three-dimensional nonlinear cyclic modelling method for non-planar reinforced concrete walls and slabs. This modeling approached - called the beam-truss model (BTM) - consists of (i) nonlinear Euler-Bernoulli fiber-section beam elements representing the steel and concrete in the vertical and horizontal direction, and (ii) nonlinear trusses representing the concrete in the diagonal directions. The model represents the effects of flexure-shear interaction (FSI) by computing the stress and strains in the horizontal and vertical directions and by considering biaxial effects on the behavior of concrete diagonals. In addition, the BTM explicitly models diagonal compression and tension failures (shear failures) under cyclic or dynamic loading. The BTM is first validated by comparing the experimentally measured and numerically computed response of eight RC walls subjected to static cyclic loading, including two non-planar RC walls under biaxial cyclic loading. Then, the BTM is extended to modeling slabs and validated with a two-bay slab-column specimen. Finally, the BTM is validated by comparing the experimentally measured and numerically computed response and failure mode of a 5-story coupled wall RC building under seismic base excitation. The final chapter presents the 3D response history analysis of two 20-story RC core wall buildings subject to a strong near-fault ground motion record. The 20-story building model includes the RC core wall, post-tensioned slabs, and columns; the core wall and slabs are modeled using the developed BTM while the columns are modeled with fiber-section beam-column elements. The two 20-story RC core wall buildings considered have similar geometry: one is conventionally designed to develop plastic hinging at the base of the core-wall, and the second is designed with a damage resistant structural system that combines two seismic isolation planes. Analysis is conducted using the two horizontal components of the historical TCU52 ground motion recorded 0.7 km from the fault plane of the MW7.6 1999 Chi-chi, Taiwan earthquake. The seismic response and damage of the two buildings is discussed.