Stewart and Oke (2012) recently proposed the concept of Local Climate Zones (LCZ) to describe the siting of urban meteorological stations and to improve the presentation of results amongst researchers. There is now a concerted effort, however, within the field of urban climate studies to map the LCZs across entire cities, providing a means to compare the internal structure of urban areas in a standardised way and to enable the comparison of cities. We designed a new GIS-based LCZ mapping method for Central European cities and compiled LCZ maps for three selected medium-sized Central European cities: Brno, Hradec Králové, and Olomouc (Czech Republic). The method is based on measurable physical properties and a clearly defined decision-making algorithm. Our analysis shows that the decision-making algorithm for defining the percentage coverage for individual LCZs showed good agreement (in 79–89% of cases) with areas defined on the basis of expert knowledge. When the distribution of LCZs on the basis of our method and the method of Bechtel and Daneke (2012) was compared, the results were broadly similar; however, considerable differences occurred for LCZs 3, 5, 10, D, and E. It seems that Central European cities show a typical spatial pattern of LCZ distribution but that rural settlements in the region also regularly form areas of built-type LCZ classes. The delineation and description of the spatial distribution of LCZs is an important step towards the study of urban climates in a regional setting.