Architecture reflects social aspects of past communities. Structure attributes such as shape, size, building material and decoration, provide valuable information beyond their immediate structural function. However, while attributes such as size can be measured and therefore objectively compared between structures, the comparison of shape between structures is based on subjective observations. In the current study we use two quantification methods for analyzing prehistoric shape-based architectural data: (1) we developed a new method, Shape Reproducibility (SR), based on objective computerized procedure for analyzing the similarity and difference between shapes of ancient buildings; and (2) we use Continuous Symmetry Measure (CSM), a method which was originally developed for analyzing flint artifacts and ceramic vessels to objectively compare between shape symmetry. Applying these methods to settlement data of the Chalcolithic period enables quantification of the level of architectural similarity within and between different sites and their comparison to architectural data of later periods, such as the Early Bronze Age II urban center at Arad. Our CSM results suggest that the symmetry of architecture does not increase through time. Our SR findings demonstrate that in the main cultural Chalcolithic entity, the Ghassulian, the architecture of different sites could not be distinguished from one site to the other. In addition, we demonstrate that the architecture of the Chalcolithic sites in the Golan Heights is homogeneous and significantly differs from other Chalcolithic sites, while Ghassulian intra-site variability is higher. In comparison with Arad, however, this variability is relatively low and limited. These results suggest that status differentiation or hierarchical social organization cannot be indicated from Ghassulian architecture.