Several simplified approaches for the damage evaluation of masonry structures subjected to base settlements are available in literature. These approaches do not take explicitly into account typical features of historic buildings, such as complex layout, ancient materials and construction techniques. The finite elements method allows accurate linear and nonlinear modelling, but usually the level of damage cannot be directly calculated. This paper aims at proposing a methodology based on damage mechanics, in order to correlate a damage functional, calculated by means of a finite elements model, to suitable damage categories. Linear models can be used, providing their conditions of reliability. The parameter equivalent strain, formerly proposed for concrete, has been suitably applied to masonry. Several finite element codes include damage functionals, in the present paper the ADINA software has been used and the corresponding formulation has been simplified in terms of equivalent strain. Both compressive and tensile damage functionals can be defined, but the last one is more able to describe typical damage to masonry buildings. Due to the fragile behaviour of the masonry, the maximum value of the damage functional typically is attained in many points of the structure. Thus, a mean value of the functional over a suitably selected domain has been proposed, in order to distinguish between different damage states. The integration domains correspond to parts of the structure having a role in the structural behaviour (walls, spandrels). In absence of experimental data about damage to masonry in terms of crack openings (damage categories) as a function of the applied load, nonlinear finite element models have been used and a set of pseudoexperimental data has been created. Finally a correlation between the mean value of the damage functional and the damage category has been obtained. The methodology presented is intended to be used with finite element models of masonry buildings subjected to foundation settlements and a real example is illustrated. Using the proposed correlation, the damage functional can be evaluated in the above mentioned domains and the corresponding damage category is estimated.