A large-eddy simulation (LES) was conducted to investigate the effects of building-height variability on turbulent flows over an actual urban area, the city of Kyoto, which was reproduced using a 2-m resolution digital surface dataset. Comparison of the morphological characteristics of Kyoto with those of European, North American, and other Japanese cities indicates a similarity to European cities but with more variable building heights. The performance of the LES model is validated and found to be consistent with turbulence observations obtained from a meteorological tower and Doppler lidar. We conducted the following two numerical experiments: a control experiment using Kyoto buildings, and a sensitivity experiment in which all the building heights are set to the average height over the computational region h all. The difference of Reynolds stress at