This paper reports on temporal and spatial variability of local climate and outdoor human thermal comfort within the Rotterdam agglomeration. We analyse three years of meteorological observations (2010–2012) from a monitoring network. Focus is on the atmospheric urban heat island (UHI); the difference in air temperature between urban areas and rural surroundings. In addition, we calculate the Physiologically Equivalent Temperature (PET) which is a measure of thermal comfort. Subsequently, we determine the dependency of intra-urban variability in local climate and PET on urban land-use and geometric characteristics. During a large part of the year, UHI-intensities in densely built areas can be considerable, under calm and clear (cloudless) weather conditions. The highest maximum UHI-values are found in summer, with 95-percentile values ranging from 4.3 K to more than 8 K, depending on the location. In winter, UHI-intensities are generally lower. Intra-urban variability in maximum UHI-intensity is considerable, indicating that local features have an important influence. It is found to be significantly related to building, impervious and green surface fractions, respectively, as well as to mean building height. In summer, urban areas show a larger number of discomfort hours (PET > 23 °C) compared to the reference rural area. Our results indicate that this is mainly related to the much lower wind velocities in urban areas. Also intra-urban variability in thermal comfort during daytime appears to be mainly related to differences in wind velocity. After sunset, the UHI effect plays a more prominent role and hence thermal comfort is more related with urban characteristics.