In this study, a method of simulating the turbulent boundary layer over rough surfaces was presented for the prediction of wind characteristics over urban areas for the purpose of wind resistant design. Using a numerical method presented in a previous paper, entitled optimization of roughness parameters for staggered arrayed cubic blocks using experimental data, the performance of the turbulence model which introduces the surface roughness effect, i.e. buildings and houses on the ground, was examined. Three-dimensional simulations of the turbulent boundary layer over modeled city surfaces in the wind tunnel were performed and the model coefficients were optimized from comparison with the experimental data. The applicability of the simulation method to the complicated surface roughness such as a real city was also checked. The configurations of houses and buildings were quantitatively obtained from maps and aerial photographs of a real city showing representative configurations of urban areas. The characteristics of the configurations of roughness elements were examined, and the discussion included what kind of parameters would be applicable to evaluation of the roughness configurations in the complicated rough surfaces, such as urban environments. Finally, a three-dimensional simulation of wind flow over a real urban area was carried out. By comparing the calculated result with the field data, the simulation method presented here shows a good applicability for the prediction of the mean wind speed and the turbulent kinetic energy over real cities. It is useful for wind-resistant design of buildings and wind environmental assessment in urban areas.