The paper presents the results of site effects investigation at two villages, Castelvecchio Subequo and Castel di Ieri (Central Italy), located about 2 km from each other, on top of carbonate ridges characterized by complex geological/structural characteristics. Both villages suffered of an anomalous high damage degree determined by the Mw = 6.1, 2009 L'Aquila earthquake, highlighting the occurrence of significant ground motion amplification phenomena. Studying seismic response at rock sites characterized by complex geological setting is a challenging issue, as different factors can alter the expected ground motion. The difficulties arise from both the reconstruction of a suitable and thorough geological/geotechnical subsoil model and limitations of geophysical and numerical methods in such contexts. In order to overcome these difficulties, we here proposed an approach which integrates numerical modelling, based on the definition of a subsoil setting built from an accurate geological field analysis, with active and passive geophysical techniques. In particular, the calibration of numerical models based on transfer functions computed from Standard Spectral Ratio applied to noise recordings provided encouraging results.