This paper reviews aspects of fault geometry and geological structure that cause spatial variations in the level of ground motions expected from large-scenario earthquakes. These conditions include style of faulting, differences between surface faulting and buried faulting earthquakes, rupture directivity effects, basin effects and basin edge effects. These effects are illustrated in large-scale ground motion simulations of scenario earthquakes on the Puente Hills Blind Thrust and the Southern San Andreas fault. The impact of these effects on probabilistic seismic hazard is also explored by means of CyberShake calculations in which the ground motions at a given site from a very large number of earthquake scenarios are represented by simulated time histories in place of conventional ground motion attenuation equations used in probabilistic seismic hazard analysis. We find that the seismic hazard estimates are quite similar in some locations, such as downtown Los Angeles, but quite different at others, such as Whittier. These differences are attributable to the coupling of rupture directivity and basin effects that are present in the CyberShake and TeraShake calculations but not in the conventional attenuation relations.