S U M M A R YThe detailed wave propagation characteristics and the spatial distribution of site effects in the metropolitan area of Thessaloniki are studied using a 3-D finite-difference method. Fourier amplitude spectra (FAS) and standard spectra ratios (SSR) are computed for various scenarios and their spatial distribution is examined throughout the Thessaloniki metropolitan area, in order to study the spatial variability of site-response. The variability of the contribution of different model layers in site amplification at different frequency windows and the identification of high amplification areas due to the presence of trapped waves in the surficial layers of the model identified along selected cross-sections, verify the impact of the complex 3-D wave propagation on the computed synthetics. Moreover, examination of the spatial distribution of the fundamental period (T SSR 0 ) from synthetic SSR and comparisons with results from ambient noise measurements show that for (thicker soil formations) the average H/V results for the fundamental period from ambient noise measurements, T Noise H/V , tend to overestimate (by roughly 30-35 per cent) the average fundamental periods from 3-D synthetics, T 3-D . The characteristics of the computed time-series and the type and properties of the dominating seismic waves are also examined along the same typical cross-sections spanning the study area, revealing the selective propagation of Love surface waves for various seismic scenarios. The previous results, as well as the strong spatial and interscenario variability of various measures of seismic motion such as Fourier spectra, peak ground velocity, cumulative energy and Housner intensity show a complicated 3-D wave propagation pattern, affecting the final site-effect distribution, both in the time and frequency domain. In most cases, even for areas with relatively simple shallow structure, the final site-response strongly depends on the seismic source characteristics, indicating the necessity of specific earthquake scenario 3-D synthetics for the study of complex 3-D geometry sedimentary basins, such as the broader Thessaloniki region.