In restoration works compatibility requirements of repair mortars are defined based on the original mortar characteristics, but the efficiency and the performance of the repair mortars after application on masonry are not generally evaluated. From this perspective, original mortars and repair mortars from two historic masonry structures were analyzed for their characterization. Compatibility of the repair mortars with the historic mortars is investigated in terms of chemical, mineralogical, and physical point of view. The efficiency of the analytical techniques used for the mortar characterization is discussed. A methodology relying on a basic approach for a mortar analysis is adopted taking into account the added values and the basic requirements from both practical and scientific point of view. This study will contribute to the existing knowledge on mortar analysis and will provide new insights on the assessment of the compatibility of the repair mortars.