The process of historical building conservation includes the repair of mortars eroded due to material and environmental factors. Identification of old mortar constituents is necessary to enable duplicating the material. Information on the binder and aggregate types and contents can be obtained from microscopic observation used in combination with instrumental methods. This paper presents the results of microstructure and mineral composition tests of mortars collected from the walls of thirteenth century buildings. A combination of techniques was used, which included X-ray diffraction, transmitted light optical microscopy and scanning electron microscopy with micro-area elemental composition analysis. The test results revealed porous lime and sand mortars with a binder-aggregate ratio often beyond the commonly adopted values. The mortars contained sand grains of up to 0.5 mm and larger pieces of limestone, flint, feldspar and brick. Transmitted light optical microscopy and scanning microscopy were found to be essential techniques for mortar characterization in existing buildings and structures.