The village of San Gregorio (L'Aquila, Italy) was severely damaged by the April 6, 2009 earthquake. San Gregorio is situated at the base of a carbonate relief bounded by the Aterno river alluvial plain. The geological features of the area are very complex: jointed carbonate bedrock, cemented gravels and alluvial fan crop out in the village. Co-seismic ground fractures were seen along SW dipping active fault segments crossing San Gregorio. We integrated the microzonation studies with new geological, geotechnical and geophysical data for supporting the reconstruction planning of the village. Noise measurements show strong and polarized peaks in the horizontal-to-vertical spectral ratios (H/V) in the 3–7 Hz frequency band. Interestingly, the alluvial fan and the outcropping rock masses show both H/V peaks. To understand the influence of rock mass joint condition on site effect, we performed structural surveys on carbonate bedrock to look for a possible correlation between rock fracturing and ground-motion amplification.