Properly accounting for the uncertainties in predicting ground motion parameters is critical for Probabilistic Seismic Hazard Analyses (PSHA). This is particularly important for critical facilities that are designed for long return period motions. Non-ergodic PSHA is a framework that allows for this proper accounting of uncertainties. This, in turn, allows for more informed decisions by designers, owners and regulating agencies. The ergodic assumption implies that the standard deviation applicable to a specific source-path-site combination is equal to the standard deviation estimated using a database with multiple source-path-site combinations. The removal of the ergodic assumption requires dense instrumental networks operating in seismically active zones so that a sufficient number of recordings are made. Only recently, with the advent of networks such as the Japanese KiK-net network has this become possible. This study contributes to the state of the art in earthquake engineering and engineering seismology in general and in non-ergodic seismic hazard analysis in particular. The study is divided in for parts. First, an automated protocol was developed and implemented to process a large database of strong ground motions for GMPE development. A comparison was conducted between the common records in the database processed within this study and other studies. The comparison showed the viability of using the automated algorithm to process strong ground motions. On the other hand, the automated algorithm resulted in narrower usable frequency bandwidths because of the strict criteria adopted for processing the data. Second, an approach to include path-specific attenuation rates in GMPEs was proposed. This approach was applied to a subset of the KiK-net database. The attenuation rates across regions that contains volcanoes was found to be higher than other regions which is in line with the observations of other researchers. Moreover, accounting for the path-specific attenuation rates reduced the aleatoric variability associated with predicting pseudo-spectral accelerations. Third, two GMPEs were developed for active crustal earthquakes in Japan. The two GMPEs followed the ergodic and site-specific formulations, respectively. Finally, a comprehensive residual analysis was conducted to find potential biases in the residuals and propose models to predict some components of variability as a function of some input parameters. / Ph. D.