A methodology for assessing site effects in cities is presented, which is based on the geometry of the prevailing geological formations and their relation to soft soil deposits. Based on a geological interpretation for the area of the city, the elevation (above sea level) of geological contacts is defined, and a three-dimensional geometric model of the subsoil of the city is obtained. The geotechnical information available is used to map soil types to the geometric model. The static and dynamic characteristics of the soil are defined as random variables and their probability moments are calculated using statistics on the geotechnical data available. A computational rectangular grid must be defined over the city and for each node synthetic stratigraphies are constructed with geotechnical parameters obtained following their probability distributions. The dynamic response is calculated for each node of the grid, by a 1D nonlinear analysis (linear equivalent) using a set of Fourier amplitude spectra generated at bedrock level using a source spectrum model, for different combinations of moment magnitude and rupture distance. Site-specific attenuation functions are generated and used to calculate seismic hazard at surface level. Uniform hazard spectra for 475 years return period are obtained. From these spectra harmonized design spectra to the NSR 10 are generated by random search of Fa and Fv parameters to ensure optimum fit. Following this methodology a site effects model for the city of Bogotá, Colombia, is constructed. This is used to exemplify trhee main direct application: i) obtaining transfer functions of the response spectrum for risk assessment, ii) generating Shake- Maps for emergency response purposes, and iii) the seismic microzonation of the city and obtaining elastic seismic-resistant design spectra.