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The study examines the degree of similarity of Neolithic settlement structures in two geographically separated regions (eastern half of Bohemia, Morava River Basin) based on the analysis of 11 variables related to the environment and the settlement structures. The period studied corresponds to c. 4900–3400 BC. Although the results of most of the variables analysed using principal component analysis (PCA) do not show significant differences in the preference of settlement locations, the analysis of the individual variables points very clearly to major differences in settlement patterns. These are manifested in different settlement dynamics, accessibility to stone raw materials, and the spatial extent of occupation. The general conclusion is that although early agricultural societies are similar in general terms regarding the location of settlements, their individual aspects are quite different, which must have been reflected in lifestyles during the Neolithic.