A methodology for the seismic vulnerability assessment of historical monuments is presented in this paper. The ongoing work has been conducted in Tunisia within the framework of the FP6 European Union project (WIND-CHIME) on the use of appropriate modern seismic protective systems in the conservation of Mediterranean historical buildings in earthquake-prone areas. The case study is the five-century-old Zaouia of Sidi Kassem Djilizi, located downtown Tunis, the capital of Tunisia. Ambient vibration tests were conducted on the case study using a number of force-balance accelerometers placed at selected locations. The Enhanced Frequency Domain Decomposition (EFDD) technique was applied to extract the dynamic characteristics of the monument. A 3-D finite element model was developed and updated to obtain reasonable correlation between experimental and numerical modal properties. The set of parameters selected for the updating consists of the modulus of elasticity in each wall element of the finite element model. Seismic vulnerability assessment of the case study was carried out via three-dimensional time-history dynamic analyses of the structure. Dynamic stresses were computed and damage was evaluated according to a masonry specific plane failure criterion. Statistics on the occurrence, location and type of failure provide a general view for the probable damage level and mode. Results indicate a high vulnerability that confirms the need for intervention and retrofit.