The microtremor horizontal-to-vertical-spectral-ratio (HVSR) technique is widely used in the urban environment to assess the fundamental frequency response of the ground. Extensive literature exists about case histories using HVSR for microzonation in several cities, but no systematic studies have been devoted to check the presence of soil–structure interaction effects, and even less attention to study building behaviour after earthquake damage. To evaluate the above-mentioned effects, a series of experiments are reported in this article. We first made a series of microtremor measurements on buildings and civil structures to evaluate the reliability of fundamental frequency determinations. Then, we considered several case studies to evaluate the effect of soil–structure interaction in estimates of site response in the presence of tall buildings. Finally, an experiment on the frequency change due to damage was performed. It was possible to confirm that HVSR is able to detect building fundamental modes and once known the building frequency, it is also possible to detect the presence of soil–structure interaction. Thus, once the presence of the building natural frequency is identified, it is possible to infer the site response from free field measurements. We also found that the HVSR technique is equally useful for detecting structural damage by determining the frequency shift of the buildings.