This article focuses on the description of material properties of segments of masonry structures in three-dimensional analyses. It mainly considers degraded and damaged multi-leaf masonry walls. In the beginning, the causes of degradation and damage to masonry are described with examples. It was reported that the analysis of such structures is difficult due to the adequate description of the mechanical properties in the individual segments of the structure and the amount of computational cost of large three-dimensional structures. Next, a method of describing large fragments of masonry structures by means of macro-elements was proposed. The formulation of such macro-elements in three-dimensional and two-dimensional problems was given by introducing limits of variation in material parameters and damage of structures expressed by the limits of integration of macro-elements with specified internal structures. Then, it was stated that such macro-elements can be used to build computational models by the finite element method, which allows the analysis of the deformation–stress state, and at the same time, reduce the number of unknowns in such issues. A strategy for performing analyses and examples of practical applications in masonry analyses were proposed. It was reported that the results of the analyses can be used to plan the repairs and strengthening of structures. Finally, the conducted considerations and proposals were summarised, as well as examples of practical applications.