The post-earthquake rehabilitation and retrofitting of historical structures is an important issue in the entire Mediterranean basin, which is characterized by its richness in historical masonry structures as well as its high seismicity. For the restoration of historical structures and monuments, high demands are raised, due to their great significance as cultural heritage carries. The high importance of these structures, the need for evaluation of their present state and often the determination of the extent and the possible ways of reinforcement, impose the development of a methodology that could offer an estimation of their behaviour, taking into account the uncertainties that are introduced during the analysis. These uncertainties caused by the variety of structural materials used in the same monument, the difficulty of determining their mechanical properties and the random action and intensity of the earthquake phenomenon make essential the presentation of the vulnerability assessment presented in probabilistic terms. This is being accomplished by a methodology which leads to the construction of the fragility curves that can graphically represent the probability of certain damage ranks under the effect of various earthquakes intensities. Through this family of curves, it is possible to investigate the way that each factor affects the vulnerability of the structure, relatively to others. The application of the methodology proposed is illustrated through three typically buildings made of masonry, situated in Crete, Greece and constructed between the 18th and 19th century. Through these case studies the correlation of the earthquake intensity is being shown.