For the first time, a high-density macroseismic survey has been carried out in the city of Palermo, Italy, after the 6 September 2002, M w 5.9 earthquake. The aim was to investigate the spatial relationships and correlations between intensity data and surface geology. A very dense database has been created to store a large amount of macroseismic, stratigraphic, and geotechnical information. A Geographic Information Systems (GIS) tool, called City-GIS, enables data processing by instruments and research keys devoted to seismic hazard. The results show the feasibility of such procedures, especially for large cities where the surface geology critically influences the ground motion. Our analysis, made on the basis of more than 2000 intensity observations scattered in the Palermo urban area, demonstrates the role of the variable geology in the variability of shaking. Significant variations of intensity are related to the geometry of the geologic formations present in the area. Intensities increase by about one intensity class inside those city sectors where the stratigraphic succession is characterized by a thin layer of calcarenites overlying very thick layers of silty clayey sands. Major amplification of up to two classes occurs in alluvial deposits in the southeastern part of Palermo, as expected. These results extend our knowledge of the seismic response in the outskirts of Palermo, which until now, was limited to the city center.