The Bovec basin, which is filled with glacial and fluvial sediments, has recently been struck by two strong earthquakes (1998 and 2004) which caused extensive damage (VII–VIII EMS-98). Strong site effects resulted in large variations in damage to buildings in the area, which could not be explained by the surface variations in Quaternary sediments. The microtremor horizontal-to-vertical-spectral ratio (HVRS) method was therefore applied to a 200 m dense grid of free-field measurements to assess the fundamental frequency of the sediments. Large variations in the sediment frequency (3–22 Hz) were obtained, with most of the observed values in the range 6–12 Hz. The observed frequencies cannot be related to the total thickness of Quaternary sediments (sand, gravel), but can be explained by the presence of conglomerate or lithified moraine at shallow depths. The results were compared also with the velocity structure derived from seismic refraction data. Microtremor measurements performed in several two and some three- and four-storey houses (masonry with RC floors), which prevail in the Bovec basin, have shown that the main building frequencies in the area are in the range 7–11 Hz. This indicates that damage to houses in both earthquakes in some parts of the basin was enhanced by site amplification and soil-structure resonance. Areas of possible soil-structure resonance were identified in the settlements Bovec–Brdo, Bovec–Mala vas, Čezsoča and Kal-Koritnica. Considerable changes in fundamental frequencies within short distances were established in the town of Bovec. Their values are as high as 22 Hz in the central part of the town, but diminish to 6–11 Hz in the adjacent Brdo and Mala vas districts. This is in agreement with the distribution of damage in both earthquakes, which was considerably higher in Brdo and Mala vas, although the houses in the central part of the town are older. Microtremor investigations have proved an effective tool for assessment of site effects in cases of complex geological structure commonly encountered in young Alpine basins filled with glaciofluvial sediments which are partly cemented. Lithified layers can considerably change the fundamental frequency and, consequently, the site effects. By taking additional measurements in buildings possible soil-structure resonance can be identified.