<p>Current seismic design practices for numerical or experimental simulations are mainly based on unidirectional (UD) conditions. These methods did not consider the effects of bidirectional shaking on soil deposits with stratigraphic variability, potentially underestimating the excess pore water pressure generation and the resulting ground damage. This study performed three-dimensional (3D) nonlinear site response analyses to assess the effects of bidirectional and unidirectional shaking on excess pore water pressures in liquefiable soil deposits. The finite element model was validated through a free-field centrifuge test and a downhole array at the Lotung Site. The two horizontal components of each selected motion were rotated to find the maximum rotated peak ground acceleration (PGA). These two horizontal components, along with the RotD100 component, were applied to the base of each soil column for site response analysis under Bidirectional (BD) and Unidirectional (UD) shaking scenarios. A modified bidirectional shaking factor (BSF) for the factor of safety against liquefaction was proposed to account for increased excess pore water pressure due to bidirectional shaking. In summary, this study highlighted the importance of considering bidirectional shaking in liquefaction risk assessments. The proposed BSF framework was particularly valuable when cyclic resistance was derived from laboratory tests under UD loading.</p>