The evaluation of the seismic vulnerability in monumental buildings is a complex task. This is due to the inherent uncertainty of ancient structures regarding their structural characteristics and material properties that should be properly handled in their seismic assessment. Consequently, a probabilistic study considering the material and structural uncertainties is a necessary step for the seismic protection of the built cultural heritage. This paper presents the study of the seismic vulnerability of the church of the Poblet Monastery, an UNESCO World Heritage Site in Spain. The seismic capacity was studied using a Finite Element model of a selected damaged bay of the church by means of a pushover analysis. The nonlinear behaviour of masonry is described by a continuum damage model improved by a tracking technique representing the localization of cracks and the consequent activation of the collapse mechanism. A Monte Carlo simulation enhanced by the Latin Hypercube Sampling technique was utilized to estimate the effect of the uncertainties, regarding the material and structural characteristics, on the seismic performance of the structure. The developed fragility curves express the safety level and the damage expected on the structure for different seismic scenarios