A methodology for modeling site effects in cities is presented. This methodology is based on the definition of the prevailing geological formations and their relation to soft soil deposits within the urban area. Based on the geological interpretation for the city area, the elevation (over the sea level) of the geological contacts is defined, and a tridimensional geometrical model of geological formations is obtained. Available geotechnical data, gathered from an exhaustive geotechnical field research, is used to assign soil types and parameters to the previously defined geological formations. Static and dynamic soil characteristics are defined as random variables and their probability moments are computed form statistical estimations over the geotechnical data. A grid is defined over the city and for each grid node a synthetic soil deposit model is obtained with soil parameters assigned following their statistical distributions. Dynamic response is computed, for each grid node, by means of a 1D linear equivalent non‐linear analysis, using a set of accelerograms which are compatible with the seismic hazard at bedrock level for the city. Spectral transfer functions of strong motion intensities are computed at each grid site. The application of this methodology in Bogotá is presented, and results are discussed in comparison with the current building construction requirements in the city.