The increasing numbers of recordings at individual sites allows quantification of empirical linear site-response adjustment factors ( δS2 S s) from the ground motion prediction equation (GMPE) residuals. The δS2 S s are then used to linearly scale the ergodic GMPE predictions to obtain site-specific ground motion predictions in a partially non-ergodic Probabilistic Seismic Hazard Assessment (PSHA). To address key statistical and conceptual issues in the current practice, we introduce a novel empirical region- and site-specific PSHA methodology wherein, (1) site-to-site variability ( φ S2 S) is first estimated as a random-variance in a mixed-effects GMPE regression, (2) δS2 S s at new sites with strong motion are estimated using the a priori φ S2 S, and (3) the GMPE site-specific single-site aleatory variability σ ss,s is replaced with a generic site-corrected aleatory variability σ0. Comparison of region- and site-specific hazard curves from our method against the traditional ergodic estimates at 225 sites in Europe and Middle East shows an approximate 50% difference in predicted ground motions over a range of hazard levels—a strong motivation to increase seismological monitoring of critical facilities and enrich regional ground motion data sets.